good question.
flash limitations are as follows…
-when the fla grows to a huge size it starts to fall apart and become corrupted. rendering an swf can be a huge pain and flash crashing while working becomes very common.
-flash tends to lag a ton…
-no real gamepad support
DLC:
when you add dlc you basicly add a new version of the game.. not a patch. so if you get wrath you didnt get a patch, you got a totally new version of the game.
there for we cant ever patch the old isaac, because wrath is the most current build from here on out.
we also cant release basic isaac as a standalone, thats why the build in the humble store is isaac + wrath.
hope that helps