(Only had 1 game out of 18-19 where I succeeded in using a pioneer to build a city rather than an outpost)
This makes it sound like you may want to scout more aggressively and be more aggressive about training and sending out pioneers. Or you may want to try a map setting which creates a more hospitable world (e.g. Temperate instead of Desert).
My general advice is that your first city should either be a Town or a Conclave, unless it's on a great spot for a Fortress (e.g. 3/3/3 or x/y/4, and usually not even then), and your second city should be whichever of the two you didn't choose for your capitol. Whichever one of those is the Conclave ought to receive the Tower of Dominion, because that removes empire-size unrest and Towns need unrest reduction less than Conclaves since gold income is not negatively affected by unrest, whereas research income is negatively affected by unrest. Since your first Conclave is likely to be your largest and most research-productive city for a good part of the early game, it's the city where it's most important to not need to worry about increased unrest from a growing empire.
You should also be considering research in the Civics tree early rather than in the Warfare and Magic trees - Civics tree research improves your ability to research technologies and build structures and train troops and fund armies, Warfare and Magic are more for improving the stuff that Civics lets you build. I would prioritize all of the first three Civics tree technologies and Trading because this gives you all of the basic town structures (Bell Tower, Scholar, Workshop), a Wonder, and roads between cities, then look into Warfare for Leather Working. After that, you can start tailoring your research for what kinds of world resources you have available, though I personally like to keep my faction research mainly in Civics until I have Craftsmanship and Economics, and I prefer the Warfare tree early on because Iron Deposits tend to be more common and more productive than Crystal Crags, and fully kitting out warriors in Warfare-tree equipment tends to cost less metal until you get to the metal armors than fully kitting out warriors in Magic-tree equipment costs in crystal, which means that, at least early on, it's a better investment to go up the Warfare tree than the Magic tree. As an added bonus, the better versions of the Iron Mine are unlocked by the same technologies that improve the Workshop, meaning that you can produce troops and improve cities more rapidly while also accruing metal more rapidly for outfitting those troops, whereas you'd need to research two lines of technologies to do the same with crystal equipment.
The way world resources shape my research strategy is basically if I have Wild Horses/Wargs, Mounted Warfare or Warg Riding gain a bit of priority, so that I'll have the horses/wargs when I want to train mounted units. If I have Crystal Crags but don't have Iron Deposits, I'll probably focus my military technologies mainly in the Magic Tree. If I have no Crystal Crags and no Iron Deposits, both Crystal Crags and Iron Deposits, or Iron Deposits only, I'll focus my military technologies in the Warfare tree until later in the game, because Iron is so much easier to accumulate and equipping units with Magic Tree equipment tends to be expensive in crystal (however, if I do have access to both crystal and metal, I will likely pick up the technology for magic staffs relatively early, so as to have a decent ranged weapon for my trained units and not need to worry about upgrading it later). My focus for improving Crystal Crags and Iron Deposits will also favor the Iron Deposits, as Iron Deposits will provide useful amounts of resources more rapidly. If I happen to have access to good shards (Fire, Water, and Air are the ones I prefer, but only if I have a spellcaster who benefits from them), or to a good number of shards, I'll consider getting Shard Harvesting early on. If I don't have many shards, or if I only have shards of a type for which I lack a spellcaster who benefits from them, then Shard Harvesting can wait. Shard Harvesting can also wait if I'm playing a game that isn't very dependent on spellcasting support.
As far as game set-up goes, I usually play any of the standard factions with a standard sovereign. However, if I were to create a custom sovereign, I would generally want two schools of magic unlocked (but I would not spend the points on the second level of any of the magic schools except perhaps for Air, because Tutelage can be quite useful), and I would specialize my sovereign for some form of spellcasting. I prefer damage/blessing/curse spellcasters, so I'd be taking traits like Brilliant, Cautious, and Tactician, and might go for Warlock as a profession, but other people get a kick out of summoning and therefore might rather spend points on Procipinee's Crown and Sovereign Bond (the trait for a Familiar) and take Summoner as a profession. While I personally would not usually do so since I don't like to play that way, you could specialize your sovereign for some type of direct combat. Direct-combat and summoner sovereigns can gain considerably from Procipinee's Crown, by the way, since that allows you to put as many sustained enchantments on that particular unit as you can and not have to pay upkeep on the enchantments. Also, when creating a custom sovereign, don't be afraid to take a weakness - weaknesses can help you make your sovereign a little better at your chosen profession even though you lost a little bit somewhere else, and if you're playing a spellcaster sovereign you don't really have to always hit the correct target in melee if taking that disadvantage lets you get, say, Fire II + Water I, Brilliant, and Sovereign Bond. On the other hand, a direct-combat sovereign might want to take Cruel despite the faction unrest penalty because of the +1 attack.
If I were to create a custom faction, I would first want to know what I want the faction to specialize in. Choosing a Race gives you the initial bonuses for units and can unlock unit types (Henchmen, Juggernauts, and Iron Golems come from your choice of Race - Altarian, Trog, or Ironeer, respectively), as well as some unit design traits and special abilities. The race you choose will impact your custom sovereign, too, so if you want that great tactical spellcaster making an Ironeer faction might not be the best choice, while Wraiths might not be the best choice for a direct combat sovereign who is supposed to follow Path of the Warrior; on the other hand, an Amarian damage spellcaster sovereign might be one of the better damage spellcasters you could get. However, that depends on how you want to play, and how much min/maxing you want to do - there's nothing preventing an Ironeer spellcasting sovereign from being a great tactical spellcaster, but it's a little harder to fund the spellcasting. Likewise, there's nothing preventing a Wraith Warrior sovereign from being a great Warrior, but Wraiths are a little on the fragile side, and the 20 dodge bonus only goes so far in making up for that. Both of these are things that add in a little bit of extra difficulty, if that's the path you plan to go for your sovereign - it can be overcome, and it isn't that much of a penalty, but it is something to consider. As with sovereign creation, consider taking a weakness to get a bit of extra strength somewhere, but pay attention to which weakness you take - No Armor might be a problem if you intend to create armies of durable trained troops and prevents you from obtaining some of the higher-level Fortress upgrades, No Ranged Weapons prevents you from getting magic staves and can cause you difficulties on maps where it's hard to bring large numbers of melee units into play and also should not be mixed with the Master Archers strength, and so on. Also remember that some of the strengths available are essentially trade-offs - Masterwork Chainmail replaces your heavy plate armor with an improved set of chainmail, which has less defense than the plate it replaces but also less of an initiative penalty, and Light Plate does the same thing in reverse for standard chainmail. Master Archers and Enchanters both improve the power of the ranged troops you can field, but I wouldn't take both of them unless I'm playing a magic-oriented faction that has great archers (from a how-I-want-to-play standpoint, not a what's-best-in-game standpoint). You could do worse than copying Altar if you wanted to play with lots of champions, and you could do worse than copying Resoln if you wanted to have the 'feel' of a summoner sovereign without actually creating a summoning-focused sovereign - Binding and Cult of the Hundred Eyes are both good for having the 'feel' of a bunch of summoned critters in your army or as part of it. Another choice is Kingdom versus Empire, which basically defines who your friends are in-game. Empires also get access to Sions, which are sort of a lesser version of the Henchmen, and can be of any race, while Kingdoms play with a more limited set of races, and note that Binding and Cult of the Hundred Eyes rely on Empire-exclusive things to provide the full benefit (Binding doesn't provide anything from Life Shards, and Cult of the Hundred Eyes requires The Black Quire, an Empire-only Magic tree technology, to unlock the most powerful of the spiders it provides). There may be similar caveats to some of the other custom faction traits.
Threads which you may find helpful:
https://forums.elementalgame.com/446543/page/1/#3380067
https://forums.elementalgame.com/446148/page/1/#3376955
https://forums.elementalgame.com/445263/page/1/#3367254
https://forums.elementalgame.com/445788/page/2/#3386380
https://forums.elementalgame.com/447952/page/1/#3393915
https://forums.elementalgame.com/445229/page/1/#3366105
https://forums.elementalgame.com/444787/page/1/#3361967
https://forums.elementalgame.com/445631/page/1/#3370289
https://forums.elementalgame.com/444783/page/1/#3364558
https://forums.elementalgame.com/445090/page/1/#3364931
Note that those links may go to my posts in those threads rather than to the thread start. If they do, I would recommend scrolling around to see what other people have said, because my playstyle doesn't necessarily line up with what you find fun, and someone else might have said something that I didn't mention, or which more closely matches what you find fun. Also note that some of these might be a little dated.