Book size has never been a dealbreaker for me because my obsession has been with organizing books chronologically -- either in-universe chronology for the Trek books I count in my personal continuity, or publication order for everything else (well, alphabetically by author and then chronological or publication order within each author's works), or by catalog number when I worked in the university library. So I've mixed and matched books of various sizes all the time; I've never really liked it, but it hasn't outweighed my other ordering priorities. There was a time when I even had Trek comics stuck in chronologically between the books, but I finally gave that up because of the risk that they would sag or bend, even with cardboard backings in the sleeves.
The only drawback I can see to the switch to TPBs is that you'd gain less shelf space by stacking them vertically. But on the other hand, they might be slimmer than MMPBs of the same word count, so you could stack more of them.
Ha-ha, true. I was partly just joking. I'm not really too concerned as all future books will likely be Trades (I think the only exception might be if Pocketbooks ever does a hardcover again--but I keep my Hardcovers together on a separate shelf anyway). So I can continue with my system and it will just be after such and such a book they will all be trades. I think I have enough height on my shelves for Trades so that shouldn't be a problem. It would probably drive me crazy if they mixed it up, a trade, a MMPB, back again--but since they will all be the same it won't be too bad.
I keep mine separated primarily by show (Enterprise, original series, TNG, and so on) and series, like my New Frontier books are all together, or my Vanguard-Seeker novels. And in publication order (though in the early days when Pocketbooks used to do the 'Giant' novels that weren't numbered I keep those separate from the numbered novels).
Where it got a bit dicey was crossover series, like Destiny or the Typhon Pact. I had to decide did I want to keep them with a show, or separate them like I do my New Frontier books. But then because later stories, sometimes series stories, built off those books it would create a problem in the sense that they'd sort of be out of place. What I ultimately decided to do was keep crossovers that take place in the relaunch litverse with TNG. The Deep Space Nine relaunches have stayed with my DS9 collection even though there is some crossover there. And there is less Voyager crossovers so it was easier to just keep those separate. And of course Enterprise is all together (though as I noted that first Romulan War book sticks out like a sore thumb--I have the trade paperback version, I suppose I could have bought the MMPB version that came out later, but my obsessiveness isn't so bad that I'd spend an extra $8 or $9 just to make my collection look prettier).