Yep. I am confident that we will hear about all the exact same problems (assets created early on but gameplay systems being implemented very late, scope explosion that makes design difficult to manage and execute, constant engine rewrites due to bad planning, etc.) after Versus is complete.
Meh, I still don't think they've been in any kind of development hell or had lack of direction or anything like that. The "problem" is simply the fact that they are developing a massive game and they don't seem to be making any sacrifices. It's basically a game that tries to offer an RPG more comparable to Uncharted when it comes to the audiovisual/technical side of things (that is, they aren't pulling any punches with the graphics & more cinematic stuff), but with a semi-open-world-ish approach that's closer to Bethesda's games than more recent FFs and with the kind of polish FF games are known for (that is, it shouldn't be a buggy mess like Bethesda's open world games are).
Their approach seems to have been very different from the usual (which is probably possible because they've had a relatively small team doing all the preparations & tech building, not thousands of people working on it from day 1). From interviews it sounds like if they've thought up some new idea mid-development, they've gone ahead and implemented it (biggest examples probably being the shift from their original plan for a world map into something different and the change from traditional cutscenes into more interactive ones). And of course they've been improving the graphics engine all this time (implementing the lighting tech from Luminous Engine etc.). Maybe that's not the most financially wise way of developing a game, but I do think it will make Versus all the much better.
Also, I'm pretty sure you're wrong with your assessment that they'd have implemented gameplay systems very late. Nomura seemed to have some pretty good ideas of where he was taking the gameplay even in early interviews. For examples, he talked about Noctis' skills like teleporting to his sword(s), which we've now seen in the January 2011 trailer. He was also pretty clear about how Versus would be more like traditional FFs in some regards than XIII (and it is). They already talked about testing airships a long time ago and have since confirmed that they are a part of the game (and not just recently). The trailer from January 2011 shows a working version of the battle system with on the fly party member changes, different skills between characters, using enemy (war) machinery, plenty of different kinds of enemy types you can approach in different ways, taking advantage of the environments, environmental destruction, different kind of interactive cinematic scenes etc. Plus we know that Chocobos have been in for quite some time and that you can drive around in a car. These are all things that Nomura has talked about a long time ago already, so I'm pretty sure a lack of direction has never been the problem, not like how Toriyama & Kitase didn't know shit about what to do with FFXIII. The 2009 demo of FFXIII was pretty barebones, whereas the January 2011 trailer of Versus showed a diverse set of features, situations & events.
Again, the problem (at least after the early problems with the Crystal Tools were a thing of the past) is the scope of the project and how ambitious it is. They had a small team working on the game for a long time to prepare the game to be in a state where they can just start crunching out the bulk of the content of the game without having to worry about there being some technical difficulties or big changes in plans (and this seems to have happened around late Summer/early Fall 2011).
I'm not denying there hasn't probably been plenty of trial & error, but I wouldn't equate that to development hell or having a generally troubled development. Duke Nukem Forever could be said to have been in one simply because it's a fairly short FPS and it doesn't really try anything special at that. FF Versus XIII is taking somewhat long because the scope is so big and it seems like they are really trying to put all their effort into making this Nomura's be-all, end-all Final Fantasy. They are trying a lot of new things or in some cases old things but updated/-graded to today's standards, which very few games have tried to do while also having the kind of high production values FF games are known for.