let's see what we have here, shall we?
first up, we first have to open the core and discover the fate of the alpha squad. then there's your plot. now, as you have seen in the prologue, the Skylark is destroyed already. so we have to re-build it. in the meanwhile, we have the time to build a satellite. not only that, a new planet just appears there! you really think cradle would build itself like that? also, in the prologue, we see all of the Cradle's star system. where is all that stuff to build a planet coming from? asteroids? oh, come on.

this planet would be the repetition of cradle. even if you change everything (weapons, monsters, maps) we would return on the same problems in a year. and in the meanwhile OOO has done its job of creating all this stuff. I would prefer new mechanics to be implemented here than in another cradle just around the corner.

together they are able to cause an EMP blast which can cause any rescue ships to fail in doing their one job.

yes, because surely EMP have the form of purple lasers. and they surely make a ship explode. and surely a non-formed planet can do that. and also there ARE rescue ships. and our satellite is completely unaffected by EMPs.

to the other things:

-Once the new mission prologue is over,players are able to choose three classes that have significant changes to their stats.

what stats? we don't have stats. you mean attack, defense, speed ect? well, one of the main strenghts of SK is (in my opinion) that you can choose whatever playstyle you want without binding yourself to it. freedom to equip. it's a really great thing.

-Slightly different gameplay on this new cradle.

sorry, that's not vague enough. could you be a little less specific?
no, really, what do you mean? and if it's so slight why would OOO implement it?

-Players can equip special one equipment at the start of any cradle#2 mission(power shield,sword etc).This encourages players to rely on the other players' powers for better co-op.

I don't understand the first part, explain please.
as for the other part, we could do it already on what we have. a good team always rely on its members to do the job well. it's those guys that know what to do in a team not to harass the other teammates. we already have that option, nobody uses it. if everyone started getting off the "OP equipment" train and explore things like catalyzer, cutter line, or bombs altoghether, they could see that there already is roleplaying in this game, only it's optional, it depends on the gear you choose, rather than what class you choose when you don't know what the game is. if you master the weapons that we already have, there are many roles you could go in this game. only, everyone chooses the direct damage because it seems straight-up better than, say, use a catalyzer in an efficent way.
I talk about catalyzers but I actually don't own one, as much as I want a Neutralizer.

-teleportation map.

I understand what you mean, and again, I would like this to be implemented on cradle and not on another planet.

-bigger havens.

explain why we would need this, please, cause I don't see a reason.

other thingies:
why we would go to this second cradle? to destroy it? a whole planet?
how would tiers work? and equipment?

If the Architect possessed teleportation technology, then the massive, intricate network of cranes, elevators and supply routes in Cradle would not be literally everywhere you look.

Those objects you mentioned play absolutely no part in the plot of SK and are merely there for aesthetic purposes.

Teleporters have nothing to do with the plot either, they're just something that you assumed existed.
If you're going to invent random technology to attempt to cover the gaping holes in your plot, at least make sure it doesn't tear open holes elsewhere.