That old mod where you start out on an airship and it gets attacked and you get a modified but ammo-limited nemesis and you can either fight the sisters (who are impossible) or jump off the ship and transfer control over to a young Momorin with the ammo-limited snake... that was you, right? Because what I'd really like to see is a continuation of that. You put so much work into reskinning everything and making everything look new, and really did have the beginning of a fun mod and a potentially interesting story. If you build off of that quality beginning rather than starting from scratch than in the time before you inevitably run out of free time or energy to work on it you'll be able to get either a lot more finished or do it with a lot higher quality, if not both.
Barring that, reskinning and all that is certainly necessary if you want it to stand out. However, it won't make things fun by itself. I agree that just throwing enemies and stuff out is not the way to go, and having too many bosses too close together is DEFINITELY a bad way to go (cough Revorshenskal cough). One boss per level, two if the plot gives you an excuse. I've always liked mods that used the booster 0.8 more than the 2.0, especially the few (actually, to this point, one that I've played) that make it have infinite fuel; yes, I know that's something that sort of takes over the rest of the game unless you take it away after a level or two, but there's nothing wrong with taking away items either, as long as you avoid making it so that there's areas/secrets/items which can only be reached during a brief period of the game before the necessary tool disappears (even if you get it back much later). In fact, giving and taking away items is a good way of varying the gameplay.
I wouldn't mind seeing a good unarmed portion or two; almost nobody does that. It has to be the right portion though; the egg corridor (both versions) and grasstown enemies would be fun to fight unarmed, while sand zone's enemies would be boring.
Please don't give the player the polar star, and then put some further effort into making sure the player cannot rely on a single weapon. Among experienced players, the weapons basically form a usefulness heirarchy: If you have the spur, knife or nemesis, always use that (knife and nemesis having some situational exceptions of course, more for the latter); otherwise if you have the machinegun or snake, always use that; otherwise, always use the polar star with the fireball for bosses and shooting around corners. And 95% of all mods default to either the polar star, because everybody knows you shouldn't give the player anything more powerful than that until very late in the game and most mods never REACH very late in the game. Yes, it's the most balanced weapon, but it's also the weapon we've already used against everything in the game umpteen times; one of my favorite things about Jenka's Nightmare and The Wrath of Revorshenskal was that they specifically did not give you any "best" weapon (not counting that hidden knife in the former) and especially not the polar star; the bubbler is a very fun weapon to be forced to use, and both had a heavy focus on it. Jenka gave you the fireball (which can't deal with many enemies) and the missiles (with strictly limited ammo) to coexist with the bubbler (useful against anything but slow damage output), while Revorshenskal also gave you the fireball and a buffed bubbler and then later a limited ammo snake and a very nerfed machinegun (and eventually the knife). Basically, the polar star's the baseline, but if you want a mod to be really memorable you don't want it to be the main weapon. I'd rather see a mod that gives you the machinegun but ends up a bit too easy than another polar star mod, because at least it's different and fun.
Otherwise, just surprise the player with things they weren't expecting to see--enemies that don't behave like they did in the original, bosses that weren't in the original, new or very altered weapons, etc. And dress up the stuff which is still the same with new sprites, new backgrounds and new music. As I said, assuming my memory's right and it belongs to someone else, you already had a great base to build off of.
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