EDIT: Apologies to akwehhkanoo, I did not read all of their reply before I posted. Needless to say I agree in full with the serious part of that comment.
Just thinking out loud a bit...
Is there a way creation of a lot of token copies of something could be shortcut, by stacking the tokens? In other words, MTGO gets the prompt to (say) create 64 treasure tokens. Instead of pooping out 64 individual cards and potentially crashing the game, instead populate the board with 10 cards: 4 individual treasures, and 6 token cards that have a big "10" on them to denote 10 treasures. Or perhaps 14 individual treasures and 5 10x pieces, but you get the idea - limit the number of individual copies to a number that the system can handle and stack the rest for use as needed. Players would have the option to (or the system would automatically) break the 10 blocks if needed to pay costs or use creature tokens for attacking/blocking/convoking etc. If this worked, stacking 100 or even 1000 tokens into a single could be a possibility, though I don't see much need for tokens totaling 1000.
I'm sure this breaks something else, but it seems a lot more preferable than how things currently work. I would prefer even a relatively small token limit that allows the game to continue rather than the current system.