'clean' pres don't sound very good?!? - well, maybe you haven't been working on studer, stagetec or lawo desks, with millenia, grace design, crane song, dad etc. preamps or didn't get to work on projects with huge channel count - but feel free to use whatever you want and add 'coloration', saturation and whatnot on end! i try not damaging the signal integrity in any way if i don't have to (which is often the case though)...
in terms of formats, the need to use multiple aoip formats depends on the scale of the situation: if you're broadcasting from a large festival, be prepared to have multiple format converters availabe or you might get into troubles - currently, i have these formats in use:
cobranet, ethernet, rocknet, reac, aviom, gigace, aes50, dante, aes67, ravenna, avb.
(i'm shocked: i though it would be but seven different formats?! and i haven't yet been counting different other formats such as adat, tdif, aes...)
if i'm on my own, i'm using my studer desks/preamps with madi throughout (well... - kinda but beyond the scope of this thread) and try avoiding any aoip. now madi can get transmitted in a variety of ways too and cables/plugs/connectors vary a lot: coax/bnc, cat cables, multimode fiber or singlemode on sc, st, lc, opticalcon duo or quad etc.