Agreed. Flamethrowers were mainly a terror weapon used to not only clear out bunkers and pillboxes but to also frighten and demoralize enemy troops. One of the reasons you don't see them in any military (Aside from being ruled as 'inhumane') is that they're nowadays impractical and more of a liability to a squad than an asset.
Back to topic.
Minigunner Infantry
For GDI, I'd think either the StG. 77 (Steyr AUG), L85A2, L86A1 LSW or the H&K G36 family would be applicable candidates for mainline arms since, all things considered, the First Tiberium War was fought primarily in Central Europe. This would mean to me that NATO would initially step in with Britain, Germany, Austria, Belgium, Etc. being at the head of the early days of the campaign before being resolved into GDI as a military force.
For Nod, I'd suggest early iterations of the Kalashnikov line like the AK-47, AKM, AK-74, and AK-74U, RPD, and the PKM. To me, these would be more commonplace weapons considering that many countries in the former USSR were either taken over by or were sympathizers of Nod. Now, I'm not buckling on this and giving Nod exclusively Soviet Arms but the only way I can logically see Nod acquiring thousands to tens of thousands of advanced small arms would be to raid military bases and the like. That considered, did happen in the game IIRC but later on in the Nod Campaign.
For Commando
This'd be a little easier for me to come up with. For the Commandos, I could see them being outfitted with a PSG-1 or a modded StG. 58 for sniping for GDI. CQB situations, I could see them using an MP5K or a Styer TMP.
For Nod, I'm kinda leaning to the SVU or KVSK sniper rifles and either an OTs-23 'Drotik', OTs-33 'Pernach', or the Beretta 93R machine pistols.
Yes, I know I didn't include scatterguns for the commandos because mainly, European countries focus on utilizing machine pistols or SMGs for CQC situations.
Also, for posterity, the Calico M960 and M100 (.22 cal variation) were initially conceived for prison guards, law enforcement and military. These guns have an unorthodox helical clip design that feeds from the top down. In addition if I recall, the M960 was chambered to 9x19 Parabellum which is effectively useless anywhere past fifty (50) meters.