I think the limit for the levels would be 100, after I took a look at the Wiki. Maybe stages might be 10 I think, but I'm not sure if it would be.
Game modes are still limited to 10 but entries or to be specific, levels, select and scenes are no longer limited. Our GIJoe mod has more than 100 entries but it still works. D&D mod has even more than that
A good portion of it depends on your preferences; for a conventional beat em up, I'd say anywhere between 6-9 stages is a good amount.
I agree with this. KoV (the 1st one) has many levels and I lost my playing mood and spirit after playing couple stages. I'm playing in emulator which allows save states so I could use these to save my progress but if I played this in real arcade machine, I'd stop somewhere

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A commercial game that's guilty of this is Power Rangers: The Movie on Genesis. I've never even completed the first level. Why? Because the very first group of enemies lasts almost 5 minutes.
I finished this game but I agree with you that it has bad level design. What really made me bored sick is first stages only have oozemen as enemies. You'll meet new enemies later but you'll never meet oozemen anymore.
New enemies don't offer better gameplay either. The repetition is still there til the end.
This reminds of The Tick, if you want to play this game, I HIGHLY recommend using emulator with save states. It's ridiculously too long with too much repetitions.
Back to topic, in my opinion it depends on how you want players to play your mod. Do you want them to play and finish it in single play (no load saved game) or play and save (use save game feature) couple times?
If the answer is the former, try keeping it around one hour. My Contra mod is designed this way. I controlled enemies' number, level length and subbosses & bosses HP & AI so it won't take too long to defeat them in early levels.
If the answer is the latter, you can be free but keep level variety and difficulty so players won't lost interest.