(No suggestions for different logo styles or more club logos - these are down to licensing issues, not much SI can do skinning/graphicaly wise)
These are some suggestions for screens/panels that don't currently have logos, but a logo could go there.
National Team Screen - Currently only the National Team badge is shown, can we have the competition (secondary) logo working in the future?
National Player Screen - Currently only shows the National Team's Competition Logo, the National Team (main) logo isn't shown currently.
Referee Screen - Nothing is currently shown, possible to add suport for a ref logo, or competition, country one?
World Screen - on the list of club/countries and transfer/awards screen nothing is shown - support for a confederation logo?
Friendly Fixtures Screen - No logo displays here either, shouldn't this just work like normal comp logos?
Support for a Third (competition) logo on match screens (and possibly the normal header) would be nice, you don't need to find somewhere to put it, I expect skinners will find somewhere just need the code supported.
Support for different Home and Away logos - some teams title bar colour will clash with the logo colours. (i.e. Swansea - home colour is white, away colour is black - logo is normaly black - doesn't show well away, same with Canada etc...) Is it possible to have the game recolour a logo?
Other places people have suggested logos could be displayed: Match Pop-ups (Goal, Yellow Card), in news items - not sure if these are a good idea, possibly have them scaled down?
Logos on the finance screen (pile of money), tactics screen (blackboard pitch) etc..., not sure where these would fit in, as a third logo on the team screen? Position could be something a skinner could solve (the Team art box in radestock's iTunes skin?)