What Should You Suggest:
Believe me....not everything fits in SharePoint....So If your organization is happy with using Share Point without heavily customizing the appearance or customizing behavior beyond what the designers and front end provides, you're probably never going to run into any problems. However, if your organization doesn't want Share Point to look like Share Point, you are about to step into a world of aggravation and headaches. To say that SharePoint development leaves much to be desired would be to play a very mean trick on those of you who haven't had to attempt it yet. If you're an enterprise Java developer, SharePoint should feel like home with it's myriad of configuration files, steps, miles of XML and use of GUIDs to tie all the pieces together. While things are getting better as Microsoft and others work on a better development toolset, it's going to be a while before custom development in SharePoint won't evoke profane muttering from even the most pious developers.
If you have to delve into the guts of the UI, you'll find Microsoft's reputation for emitting ugly HTML and bastardizing CSS holds true. SharePoint spews forth nested table driven layouts sprinkled with hundreds of CSS classes the likes of which I never imagined. Needless to say, the road to trying to amend this is itself not clearly feasible, although I have been tasked with finding a way. While I do have leads, I've got nothing concrete, nothing from Microsoft on how to and very little time to do what I need to. While your run-of-the-mill skinning and layout exercises can be done using themes and master pages without much difficulty, those who find themselves in situations like mine will find it hard to say nice things about Microsoft's SharePoint team.