Yeah, it is a pain in the ass, I admit. When using coin control you can see the current size of the transaction as you add inputs. The max size right now is 100,000 bytes. It is a good idea to occasionally combine your inputs to keep your wallet slimmed down and to allow for larger transactions when you need them. I was thinking in a future release I would bump that a bit to more accurately reflect the size of of some transactions. That would work, but is kind of a bandaid. With 1MB block size 100KB only allows for 10 max size transactions per block. A better fix would probably be some kind of auto-combine function. I am open to suggestions on how you guys would like to see this dealt with.