Homestuck?

[The Wanderer]

as far as I've been able to grok, the Green Sun is a constant that links all Sburb sessions, because each session has a 'Guardian' and they are powered by the Green Sun itself.

Both of the "main" sessions seen so far in Homestuck canon have Guardians and are tied to the Green Sun... but that latter is, at least in part, because the Green Sun was created out of those two sessions. Possibly literally; if you remember, Rose mentioned at one point that the Green Sun was nearly twice the mass of their entire universe. It's suspected that this means the Green Sun is actually composed of the total mass of both the kids' universe and the trolls' universe.

There's no definitive indication that even the Guardians, much less the Green Sun, are an inherent part of the game; there's no definitive indication that they aren't, either, but AFAIR they don't seem to have any connection with the mechanics or progression of the game per se. (However, if we do have a near-omnipotent First Guardian, who and/or what would it be? The humor option would be Pen-Pen, but there are certainly other possibilities... even if we don't have two of them, Adam and Lilith.)

I don't think the Angels make sense as Agents (or vice versa); the only way I know of for the Agents to have anything like the kind of power the Angels display would be by way of the prototyping, and that seems to only affect A: the lesser monsters (imps and ogres and so forth) and B: those wielding the implements of royalty.

One possibility would be that the Progenitors are what they canonically seem to be, the ancestral origins of human and Angelic life - but that they themselves are merely part of the universe which was created by the previous session (whatever that was), and their nature and their power is derived from that. One interesting effect of that would be that it would make it appropriate (to the point of necessity) to have both human and Angelic players, preferably in equal numbers - and hey, we already have two partly-Angelic players, in the form of Kaworu and Rei.

(At this point part of me wants to bring up the question of the god tiers, but I suspect that would have to be dealt with much further down the line, once we have some idea what the plot might be like. Unless you tie myths about ascending to the god tiers into the quest for Instrumentality...)

Players = Shinji, Asuka, Kowaru, Rei, Toji, Hikari, Kunsuke and Mana.
Pardox Clones: Gendo and Yui Ikari, Kyoko Zeppelin Sohryu, Khiel Lorenz... need two more.

Why do you need only two more parent/guardian figures? In Homestuck canon, each player had exactly one guardian. (And the players and guardians alike were paradox clones, created as infant copies/recombinations of their older selves. See the MS Paint Adventures Wiki entry on Paradox Clones for details.)

I suspect that Kaji would be at least as likely a "guardian" figure for Asuka as Kyoko would - though I'm not sure where Misato would fit into it at all. (Also, remember that by Homestuck canon, the guardians all end up dead after the session gets underway. Though that's at least partly due to Homestuck plot events which probably wouldn't have any direct equivalents in such a crossover.)

Who do you guys think should get what titles? Right now we got more titles than players.

I'm not quite sure what you mean by that statement. We have established templates for titles, but we don't have to - and probably shouldn't - use the same titles as in Homestuck canon; we should follow the same sort of pattern, this is one place where creativity and originality is not merely possible but all but required.

Also, in considering that, we'll eventually need to work out names for the players' associated planets; keep in mind that there's a pattern to those names too, tied to the players' respective titles. (Heir of Breath / Land of Wind and Shade, breath matches wind; Knight of Time / Land of Heat and Clockwork, time matches clockwork; Seer of Light / Land of Light and Rain, light matches light; Witch of Space / Land of Frost and Frogs, space matches frogs.)