As you progress through the chapters in Moscow, you have to make a choice between siding with the Vory or the Mafiya. It appears that you can freely choose whichever side you want each Episode; you can side with the Vory in Episode 1 and then side with the Mafiya in Episode 2. Here are the known differences between the two tiers, broken down by Episode:
Episode 1, Baklany:
In chapter 2, there is one job difference between each side:
The top job, Collect the Ransom, is Vory only, while the Collect the Hit Payoff job is Mafiya only. Here are the two different items possible from this job:
And the Molotok Pistol is Mafiya Only.
As you can see, the only difference in Episode 1 in choosing a side is if you want access to a bad vehicle or weapon. The Mafiya pathway costs more money (you need 6 Takis which are 1,000,000 Rubles) while in the Vory pathway you only need 3 Taksis (you need 6 Mototsyki which are only 500,000 Rubles a piece). On the other hand, The Mafiya pathway is more efficient (1.71 xp per energy vs 1.68 xp per energy). It really makes no difference.
Update: This is the job mastery reward for episode one for both Vory and Mafiya, so really for the first tier there is no significant difference between job paths.
And yes, another combat item... /yawn.
Episode 2, Boets:
There are more significant differences between the path you choose at this stage, although it does not seem to make too much of a difference yet:
Differences in Jobs:
Well, as you can see, not too much of a difference. The vehicle is a little bit better than the weapon, but if you have a fleet of Track Loaders / Hu-9's / Armored State cars, it does not matter.
There are different jobs between each tier that you can see in the pictures above. One thing to note is that the differences in payment between jobs is potentially due to differences in bagmen between characters. One main difference is that Vory is required to use Concealable Cameras to work through Episode 2 does not have them required. Other than that, it is too early to call until we see if the job mastery reward items are different (I am guessing they are not).