Zen,
I understand your reasoning but your basis is flawed. As Zaphide said, the main content of Exerelin is its world generation and faction mechanics that provide a unique experience that the original Starsector doesn't provide on its own. The added factions are simply a favor done by Zaphide to allow players to take advantage of Exerelin with other popular mod factions, which may be cumbersome to do on your own. He was even kind enough to provide a very simple 3 second method to remove any factions that players may not like. In fact, this whole mod is a favor done by Zaphide to the Starsector community and he has absolutely no responsibility entitled to his work because its voluntary (except for maybe asking for permission for use from other modders, which he is doing very well). It's completely different from professional game makers who have to take responsibility of their product for sale.
As for the actual faction balances, I really see no huge problems. Sure, some ships are a bit stronger than others and some weapons are a little op, but that's it. It's nothing that you can't beat, because although they are strong, they all have weaknesses that can be strategically exploited. With this much content, it's impossible to keep perfect balance in the first place; Hell, the TriTachyon are pretty much op compared to hegemony in the original game anyway (like the indestructible hyperion?).
Depending on which starting faction you choose, the game may be difficult at different stages. If you really can't keep up, solve the problem yourself and remove the op faction. Demanding stuff from the modder can be rude at times.