There's three issues with Pets re: capacity and vehicles.
1, the design of the restraints. They are undeniably more restrictive than they reasonably should be, excluding some (but definitely not "most") guests who are right to be frustrated.
2, the length (or lack thereof) of the load and unload belts. Some of this was unavoidable due to the strange shape of the space they were working with, but the TMs are forced to stop all vehicles repeatedly due to folks needing extra time getting in and out of the vehicles. TMs tend to have just enough time to get someone in a box on the longer loading belt without a stop, but the unload belt is significantly shorter, meaning the ride almost always has to halt when someone needing accommodations reaches this area - which, of course, happens frequently. (This is of course not the fault of those who need those accommodations, but because the way the ride was designed, it really hampers throughput. I'm a little surprised this element wasn't given more consideration during the design phase, but I suspect they decided "virtual queue!" would solve all problems.) While I don't think Pets will ever end up anywhere else since it's a dormant/low-priority franchise, if they do attempt to use this ride system again, I expect a layout that includes much longer belts (or a single, lengthy load/unload belt like California Adventure's Little Mermaid ride).
3, the number of RVs. Yes, people are continuously loading, but it's at a trickle, not a steady stream. The boxes are more spaced out relative to other omnimover-like rides due to the adoption scenes near the end of the ride. If the RVs were more tightly packed together, you'd see huge improvements in capacity, but that sequence would become unintelligible (and inevitably less personal) with the sound bleeding between groups. One could question whether the execution of the adoption scene warrants the RV sacrifice, but here we are.