Well, I think you should do whatever your Pokemon would like to do! I'm sure they wish to have fun as well, and so whatever would be best for them to do so, you should do it!

There shouldn't be any problem with them standing out. That makes them different, and there is never anything wrong with that! Besides, think of how cute they would look if they had on small, nice clothing made just for them!

If you'd like, I can show you the clothes that were made for my Audino?