Just a couple of notes - we (I say we, Dale did all of the actual work, I just ordered him about in typical woman fashion) didn't mess around at all with teams in the top two divisions. The likes of Metalist, Dinamo Moscow and Dnipro are still in the top tier, whereas nowadays they're probably suited for the second tier rep wise. Likewise, there are some bigger clubs in the second tier. The reasoning behind this is mainly just wanting to play it rather than fucking about doing yet more editing. Also, in the higher tiers where there are more promotion spots available so it evens itself out very quickly, usually the first season or two. The lower leagues will take longer to fix themselves due to promotion being from a pool of about 200 teams, so there was more focus put on replacing teams that have fallen a lot since the file was originally made in 2013. These were mainly teams that conceded 100+ goals consistently on the teat saves and won no games all season. There were 3 lower rep teams promoted (Altyn Asyr, Dordoy and Istiqlol Dushanbe) so that there's a playable team in every Soviet country from the start.
Dacia are in the wrong zone in the third tier, that's just an oversight but it doesn't seem to affect them too much, they've done well on all the test saves.
A number of the smaller teams in the third tier have almost their entire squad contracts expiring 6 months after game start. We theorised that this is due to those leagues usually running on a Summer schedule rather than Winter like sensible leagues. There are still plenty of teams that operated on a normal schedule so their contract situation is a little better.
All ex-Soviet nations are classed as non-foreign, as well as those that signed the Warsaw pact. This is basically all of Eastern Europe but NOT ex-Yugoslav countries (I found this out the hard way).
Some teams in lower tiers will be in European qualification at the start, due to them being domestic champions in their own league before the fictional reformation of the USSR. This is actually a bit of a bonus as it means you have a chance to earn a bit of extra money early on. This will fix itself after the first season.
All in all, it's a really great structure that a lot of hard work went into. It'd be perfect for a C&C game, because as you can see in the screenshots Dale posted, a lot of the smaller teams (Armenia and Belarus in particular) produce utterly fantastic regens. This is due to the clubs being based in Russia and therefore using their youth rating which is considerably higher than other ex-Soviet nations, while still producing players of the club's 'own' nationality. So when combined with some of the frankly ludicrously good youth facilities that some teams in smaller countries have, you end up with some world class regens.