I'll start with easy questions...
a.I know day and night last 24 minutes while morning and evening last 3 minutes, is there any way to change that? 24 mins is a lot if I'm making a short RPG.

b.How many days does it take for a season to change?

c.Is it possible to make a border like "town"? This means a town with two exits but without using warp points.

d.I read somewhere on GameFAQs it is possible to go underwater if you play correctly with the ground-water elevation, is that true? If so, how?

Tough one...
e.Is there anyway to go beyond the 100 People limit? I think that is way the most frustrating limitation of the whole game, 100 people is not enough at all to make a long game. So, maybe it's possible to use the same person in different areas (in a different mode so it shows a different text of course), if that is possible then RPGM3 will lose probably it's biggest limitation.

f.About skills that use HP instead of MP, do they have "set" damage or does MDEF or DEF alter them? Cuz I never see a difference on "physical" skills.

That's all, and I would really appreciate some answers, it's ok if you just answer one of my 6 questions, or 2 or 3, etc. Help is always accepted ^^

I can answer the first two.

You can easily change the time and season at will. So you don't need to worry about waiting that long.

Just have an event that pushes the time forward or what not.

Well yeah, I think waiting for seasons it's almost pointless, but still 24 mins is too much for day, it's a total of 54mins-1hr for just 1 complete day. Would be cool if when you stayed at an inn you would wake up 12hrs later or something like that.
I know it's possible to make a custom inn and it's easy but eats a character slot! ; ;

I think you can do what you said about the inn. As vonwert said, you can change to day and nite in an event. I suppose you could have it change to evening at some point along the journey and then... Set a switch that turns on when you speak to the innkeeper and agree to stay the night. Then, when walking out of the inn, if that switch is on, it changes to morning and turns the switch back off.

For question C, I dont know about a town with two exits (maybe, i just dont know) but i know you can definitely do a dungeon like that if that helps. We have a border on our game that is a mtn. range with a tunnel entrance on one side and a tunnel exit on the other side and you go thru a dungeon in btw. Don't know if that would work for you or not.

yeah it did help, i used a tunnel ^^

Okay, I'll see what I can come up with.

Yeah, that is a pretty long time to wait for a day to pass, especially if you wanted something to happen that only happened on either day or night. But at least you can change the time of day with an event. Also, staying at a default inn automatically brings the time back to morning.

I don't think Seasons change automatically.

Yes, it is possible to make a border town, but there's a catch. Some towns have 4 extra areas that can be activated to be either be empty or occupied by a hot air balloon. You could have a town with one such empty area, and place an event in there that warps the player to the other side of the town.

Don't know about going underwater, but I guarentee you won't be swimming.

The 100-person limit is there and cannot be worked around so far. You can't place the same person in more than one spot, not even if they're in completely different towns. If you place Person B in Town A, Person B will no longer appear on the list of placable people. It's a stupid and very not understandable limit to be sure. If you're wanting to have a long game, expect to have sparsely populated towns.