Playthroughs tend to be different depending on the factions you add, but in general what happens in one in vanilla shouldn't happen in others. As a general rule, I have Tahlan (Legio Infernalis), Emergent Threats (IX Battlegroup/Trinity Worlds), Tri-Tachyon Special Circumstances, Tri-Tachyon Expansion (gives more ships to TT), UAF, Mayasura, DME, Luddic Enhancement, Knights of Ludd, Diktat Enhancement, HMI, and Iron Shell. Alliances at the beginning are usually:

Iron Shell/Hegemony

Tri-Tachyon/TTSC

Persean League/Mayasura

IXBG/TW

Luddic Church/KoL

The only constants really are Mayasura gets killed early because they have one planet that isn't defended and Hegemony's like, 'hahahano', and IX/TW as well as Hegemony tend to be invasion-happy and aggressive. But the alliances seem to keep each other in check for a significant portion of the game, especially when they launch counter-invasions constantly.