Variations on a theme are good, but try not to be too set on providing very similar rooms or the player may get bored (I don't think I'd want to play 10 rooms in a row which are simply dealing with different roach formations, or eyeball formations, unless there are some other factors present to spice things up) It might not matter if the rooms can be completed fairly quickly though *shrug*
Difficulty-wise, you could either go for increasing difficulty throughout the level (get the player used to a concept, and keep pushing it further and further) or else intersperse difficult rooms with moderate ones, pacing things (something like the equivalent of end of level boss and mini-bosses)
Layout. If rooms aren't incredibly difficult, your current scheme of one after another works OK (and it certainly saves on boring running backwards and forwards) If you're going to have rooms of exceeding difficulty, it might make sense to break things up a little - give the player a choice of puzzles, or make some puzzles optional, so they can leave the one they're stuck on for a while, and come back to it later.
If you're keeping to your simple arena format, and going from easy-difficult, it might be an idea to have an entrance area, giving the player a choice of arenas based on each different theme. Exiting the hold only after all arenas have been completed would present a building challenge though.
BTW, it took me many, many attempts to complete the last eyeball puzzle in v2. About the most difficult of such puzzles I've encountered so far. Great stuff
The next hardest was 7N, because...
It took me a number of variations of 116, then 115, to get there (and it shows in the demo 
) I'm thinking less is pretty unlikely, but I can probably find a hat if I'm wrong *grin*