I'm mostly intrigued with the Box System to store and take out your pokemon; its version in Shoddy 1 was rather... shoddy. It was laggy and annoying to use (I understand the lagginess was in part due to java, but honestly, the number of confirmation windows and switches made it a lot worse.) I have a couple suggestions to make the whole team creator more efficient using the box system.
Most importantly, I think a "Pokemon Creator" should be seperated from the Team Creator to make teams more easily. You would open the Pokemon Creator, and start building your pokemon - but because of the omission of the 6 different pokemon, it would be less laggy and there would be more room for other stuff. First, the EV's could be more user friendly by adding a "Max" box to each stat - it would lump the max number of remaining (or possible) EV's into the stat to avoid unnecessary addition or subtraction. Say you wanted a max att/speed with 4 hp - just click the attack, speed, and hp boxes in that order. If you wanted a 252 in one stat with various values for a few others - max out the first stat, type in one, then max out the final stat.
As for moves, (and I don't know if this is possible,) it would cut down on time slightly if STAB moves were automatically made at the top, and non-stab moves alphabetically afterwards. Pretty simple idea, but again, I've no idea if it's possible.
The same thing could be done for items, but the top couple items used (lefties, etc) could be lumped at the top for easier access.
A seperate tab could also be added; one that specifies the use of the pokemon. This would be a simple way to help organize for team building later; just include several options like Sweeper, Tank, etc. After you've finished your pokemon, and it does a scan to see if it's legal, it could be put into the box automatically for use in team builder, and if it's given a tag like Sweeper or Tank, it would automatically go into one of the boxes that has those names. This would make it far easier to visualize a team; you've got your sweepers in your sweeper box, tanks in your tank box, etc. Once you've saved a few pokemon, you could exit to the Team Builder and simply pull them out in the order you need from the boxes. The current box system (and team builder in general) has a lot of unnecessary button confirmations - since java has been known to be laggy, any attempts to compress or eliminate extra windows or messages would maximize efficiency. After you've pulled your 6 pokemon, you could possibly request a team analysis - a function that would tell you your overall team weaknesses + resistances (4 weak to ground, 2 weak to electric, etc.) Other helpful things that could assist in making efficient teams without repeatedly switching pokemon to see their weaknesses would also be helpful.
In the team builder, it would list your 6 pokemon with their moves (and function, if applicable) and be far less cramped. If you see an obvious error with a pokemon (which is a distinct possibility) opening pokemon builder again would be laggy and annoying; a possible "quick edit" button that could only change moves or items might be necessary.
I know this is a meaty post, but I figure if some of it is considered, it would increase efficiency and possibly cut down on lag, while decreasing team builder time over a period.