Personally I think Lyran is pretty tough to fly, unless you go LDR cheese.
Klingon is tough to fly
well. Anybody can compete flying Klingon, excelling at it is another matter.
Fed likewise. Real proxies would make Fed a lot more challenging to fly (as it used to be).
Rom - tough to master that cloak, but once you do you can be damn near unbeatable.
Gorn - with the exception of a few ships is a very tough race to fly. How would you like to have Ph-1 as your heavy weapon?
ISC - please.
Kzin - maybe the toughest race to fly in late era.
Hydran - it really depends, because Hydran has many flavors and each one has a rock/paper/scissors quality with every other race. Fighter cheese works well against ISC and Gorn (unless they have D or I-torps) but not against drone races. Hellbore boats work well against Klinks and Lyrans, but not Feds or ISC, etc etc.