I kind of agree and disagree at the same time with these points.
Firstly, Ratchet & Clank has always been at it's core a solid singleplayer experience. To end with a grand finale that is some sort of MMO would feel somewhat out of place if it was done in such a way that it couldn't be enjoyed just as much as the previous games in offline mode. So for this I think they would need to change the core formula a little bit. It would all be for the better though, as the games are slowly starting to lose their appeal over time.
As for story progression, imagine Grand Theft Auto (Liberty City or early San Andreas) but with 20/30 islands instead of 3. Now imagine that those are all actually locations on planets, all separated by a lack of having co-ordinates for them. So you'll start off on one and as the story progresses you will gradually unlock new locations. Each location will be quite large, and typically of a multiple path design, somewhat like what we had in the original games, but with a few more paths and larger hubs. You could find secrets, do the main missions (which result in further unlocking new locations), or do side activities and optional challenges.
Space travel like what we had in ACiT would be pretty welcome. Although it would be cool to have sectors with space stations and all sorts of space missions to set in these sectors be separated by massive voids of space. You could fly out into these voids and try to find planets on your own, but you are likely to get ambushed by more tough enemies the closer you get to these planets. If you do manage to find a planet on your own, and land on it successfully, you will likely have fought strong enough obstructions that you are more than ready to land on the planet anyway.
The galactic map would always show you where you are relative to your previous destinations, and the locations of planets you have discovered or unlocked. You could set a warp marker anywhere on the map and warp there, but if there is a planet or space station between you and it, you will be destroyed. This is unless you have discovered the planet you are warping to, in which case you will only be destroyed by known and mapped obstacles in your path.
Gameplay would be the same as it's always been, with gadgets and weapons being awarded to you after certain mission chains were completed (including side missions). But of course you can always buy weapons from vendors as you approach them. I always thought it would be cool to have two vendors too. Slim Cognito and Gadgetron (or whoever). Both offering different services.
Of course the premise for this game would just have to be some new and original plot. Whatever it is, it should take place after ITN, and attempt to tie up the series as much as possible. Like MGS4. To end the series in the Great War which took place before all the games we know today, would not feel right to me considering how ITN ended.