Eye candy: Trillian probably has the most advanced skinning mechanism I've ever seen. Sadly, advanced != user friendliness and there is a lack of good GUI tools to actually allow artists and people with a knack for UI design to sit down and create stuff. Trillian, for the moment, still requires some programming ability, as opposed to Winamp classic skins, for instance.
Quite simply, the barrier to entry is too high for Trillian skinners. This could be made a lot simpler. There are a few good skins; but not nearly so many considering the size of the community. I can just point to the Whistler series and the Aikon (not Aikon 3, which I detest) as examples of nice skins. Sometimes, complicated skins aren't necessarily the best ones.
Protocol support: Trillian obviously lags behind the latest and greatest features offered by individual IM protocols; so some additional features would be much appreciated. I do know that file transfer support in Trillian is abysmal and fails more often than not. Other nice-to-haves for Yahoo IM would include chatroom support and IMVironments (although I use neither myself). I am particularly interested in seeing how Launchcast can be supported in the Trillian client; but that might be quite hard to do, so I'm not holding my breath. MSN; well, not much to add there, since I don't use it too often. Actually, in terms of completeness, I think AIM offers features closest to the original.
Of course, Trillian already offers the quite useful SecureIM feature over ICQ and AIM; and they also support direct AIM connections. They could also be a bit more proactive in connecting to IM servers, for instance the vanilla IM clients try a variety of ports (21, 23, 80, 8080) and sometimes a variety of server addresses (for Yahoo, especially). Some work is obviously needed for the auto-update as well to prevent lots of people being locked out regularly when Yahoo/MSN/AIM decide to play hardball.
Other stuff: One thing I'd dearly love to see is an easy scripting language built into Trillian. Perhaps this is better served with the existing plugin architecture, but it would be a nice addon. TrillPerl and the WSH extension don't seem to cut it. Things like scriptable away messages, a dynamic "what am I listening to now on Winamp" status message etc would be nice additions.
But above all, the point of this rambling post is to remind CeruleanStudios of Nullsoft and their disastrous Winamp v.3 Please don't make changes for the sake of change.