I could see setting up a decent stat customization system through a means of "upgrading" gear and selecting certain stat paths. Upgrading could require some sort of reagent purchased either with Soldiery tomestones (probably the best option) or dungeon drops, or a mix of the two, and there would be a cap on the number of times you upgrade down a path so that you don't end up wearing the same piece of gear for tier after tier after tier (boring).

That said, given how shallow FFXIV's stat system is, having Allagan gear be high ilvl than tomestone gear pretty much means it's going to be BiS always (with the possible exception of BRDs who heavily rely on crit). This is STILL problematic, because I don't believe someone should be able to regularly clear Coil and conceivably never see a drop for them because RNG is a bitch. Having tomestone gear of at least equal quality primary-stat-wise means that while you're clearing Coil, at least you're also earning Soldiery tomestones that, if RNG doesn't smile on you, you can trade in for something.