Too bad this thread hasn't received any recent attention. With the possibilities of editing the game, some improvements for the SSE could be made.
My thought of approach to changing this would be (as it commonly is for most people): How do I improve the existing gameplay optimally, while investing a (comparably) small amount of effort.
Improving the story... that requires too much work on whole and will achieve little. Maybe if it's kept simple and silly it can be okay. (Methods are comic cutscenes, weird dialogues and such things... where the means to bring graphically polished results are lacking, creativity might help
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Model hacks for the generic enemies might be worth something. The new models should be similar in their behaviour to what they're replacing. That might at least give the SSE the charm of being more related to the characters specific games. Texture hacks for levels go in the direction. Levels will stay generic... so how do you give the levels a more Sonic, Mario, Zelda, etc. feel than a somewhat generic forest, desert, castle feel. It just doesn't let that fan boy "this level feels familiar (from playing SMB 100 times)" sense arise.
The important question I've read from other posts (and I guess think myself too) is: How do you give the SSE replay value?
First adapt the physics so that going through the levels feels more fluid (I guess I'm critizing that it doesn't feel that fluid now...).
Maybe backtracking levels and having to fulfill certain tasks (and those in a certain limited time) (good question what taska... I admit not to have thought so far on this point) to proceed in other areas. (That could prove a difficult thing to achieve thought
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Since boss and mini boss fights are memoriable, those can be enhanced (those boss fights are the reason I go back and pick up a game like Mischief Makers and play an hour or so).
Anyhow, if it's possible to edit the game physics (yes) and edit models and textures (a somewhat yes) and maybe choose which models are replaced in each level (that would be nice if yes were the remark to that one) then already with only a lot of work (but maybe still in the reasonable region) something enjoyable could be achieved.
Just some humble thoughts to try and keep certain people's hopes high