It seems like some of Pokemon's current problems are not really that current. Read this article from back in the WotC days.
http://www.pojo.com/CardofTheDay/110400FlawedGame.html
You could change the names of the Trainers and Pokemon and publish the same article today.
I'm not suggesting banning as a solution to the donk and short game problem that many don't like.
I do think that the core rule about losing if you have no Pokemon in play should be changed. Instead of losing when you have no Pokemon in play at the end of your opponent's turn, I think your opponent should just get to draw an extra prize card. On your turn, if you can put a new Pokemon from your hand into the active position, you play your turn normally. If you can't, your turn is over and your opponent draws one more prize card. On his/her turn your opponent would still draw and play any cards normally - other than attacking. At the end of his/her turn your opponent would then get to draw another prize card. You then start a new turn following the same procedure.
You only lose when your opponent has drawn all of his/her prizes or if you deck out.
Some may try to play with a limited or no bench and keep Pokemon in their hand. I don't think this would be a very effective strategy though, as there is still a significant penalty for having your active Pokemon in play knocked out, and none on the bench to replace it.