The most important thing I would like to be addressed is consistency between games:
* Sub5, Sub6 and Sub9's (grey) mover should look the same (right now they don't in the HD versions). This is especially important because a smooth transition from Sub5 to Sub6 needs the mover to look the same throughout the scene.
* Sub1 and Sub4's basement, Sub3 and Sub4's loop area, Sub0 and Sub5's ancient temple, and Sub2 and Sub5's lighthouse dungeons should also match.
* All karma portals should receive the updated Sub10/SubVerse look; all wisdom gems should look the same.
* As Sublevel says, all lighthouse pictures appearing in Sub1 and Sub2 should match.
* In general, any new changes made in a Sub <10 game should be reflected in its Sub10 version.
Besides all that, since the main series is now finished, it is probably a good time to revise the plot to make whatever fixes/retcons/improvements are deemed necessary, and perhaps even expand it a little (like Mateusz did with Sub3 HD). I don't really have any specific suggestions here yet.
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Some comments about the suggestions in Ko9's list:
Submachine 1 putting spoon on an electric device makes no sense.
It does make sense, but it is not obvious. An easy way to fix it would be to add a note saying something like "WARNING: Risk of electric shock, do not place any metal objects near the generator" (or the standard yellow triangle icon if you want to make it less evident).
Make it unable to escape Submachine 1 without a wisdom gem.
I don't know if this is a good idea. I think I would prefer the ability to move back to Sub1's ending from Sub2's arcade to retrieve the wisdom gem (the karma portal's sound should be there just like in Sub10, but the portal itself shouldn't be visible and the picture shouldn't be broken yet, so as not to spoil the karma portal mechanics and Basement exit location).
Fix the Submachine 2 clockwise circle puzzle.
What needs to be fixed here?
Having keys named beyond their color like '2nd floor key' makes no sense.
This is somewhat of a problem in almost all games (connection pod, iron trioxide, navigator, vector finder, handle for the X machine, etc.). I agree that it doesn't really make sense for the player to know their use in advance, but it also makes no sense gameplay-wise to name everything "unknown metal object #17". Perhaps in some specific cases like this one it can be fixed (at the expense of making the game a bit more frustrating for new players), but I don't think it is a big problem in the end. Lore-wise I guess we can assume that the player's character has been prepared by their usher before entering the Submachine and would know what most important objects are used for.
Older versions Menu List
I don't know if including playable older versions is a good idea. It would probably confuse new players, it's extra work for Mateusz, and the old base is already familiar with older versions, so I can't see how they will generate much interest overall (as opposed to the new content). Sublevel's idea of having the original SWFs seems a bit better, but I think even that is unnecessary, as they are already being saved by the Flashpoint project. The idea of having a developer's commentary for each game looks much more interesting to me.
Release a OST DLC with the demos.
Redraw notes-pictures (because they were drawn for 400x400 format)
Add a open door button to the elevator so them opening is more logical.
Submachine 2 Sewers work so that you can see the pipes above you that you aren't in, should that be fixed?
Make the device in Submachine 2 that holds the gem more obvious.
Make the shafts in the lighthouse tower ladder for the secret and negative and positive bulb more obvious.
I agree with these.