Should I upgrade commanders or buy them?

Buy the new ones. Save medals for Badoglio (1210 medal arty gen). Then try to go on for Vatutin later. You have to complete ww2 campaigns plus cold war campaigns. After that alien conquest would start. At this time build your gens. Or you can ask to Max Otto von Stierlitz if you want to upgrade your ones right from the start. Fell free to ask questions if you still have doubts.

Academy gens have much higher price/performance ratio than ECs (custom gens, which you can upgrade). ECs can become much stronger than academy gens, but that's expensive. Assuming you have only 3 ECs and you can use not more than 6 gens at once, you need at least 3 academy gens. So it's better to start with academy gens (at least Govorov and Guderian) and than build your ECs. But wisely investing some 1000+ medals in EC instead of buying Badoglio is not so bad idea (you can read about it in my topic about ECs). Further upgrades of ECs before buying academy gens are not effective, only if you want to build ECs just for fun.

ECs have to be upgraded very wisely. In fact, upgrading even 4th tank star before you have all skils at lv3 is a big mistake. Academy gens are cheaper than ECs, but investing around 1400 medals in EC before buying academy gens is quite good idea (something like 80hp, 2 art, 2 speed, 2plain, 2 barrage and 2 explosives). Btw, that is especially for beginners, as you get quite notable help from the very beginning and you don't waste medals buying gens, which you will replace later. Sure, at this point it's better to stop and buy academy gen next, but in fact this is something like Badoglio first, which lets you get medals for Govorov or Guderian much easier than buying one of them first.

Sure, it's easy to waste medals upgrading ECs, for example, 5 tank stars cost 2300 medals and give 28 damage, but 3 tank stars + plain fighting lv3 + explosives lv3 cost 1550 and that give 31 damage against units and 55 damage against cities and forts (assuming you are able to find plains everywhere and very rarely will have to attack not from plain, so 31 damage from plains is equal to 28 damage from eveywhere). So you get almost twice damage against cities and save 750 medals, for which you can add, for example, 120 hp. That's why in "looks cool" doesn't mean performs cool, but in general ECs are not so expensive, especially keeping in mind that it's more fun to make custom gens than use predefined.

If you have upgraded anything instead of plain fighting, explosives, supply, tide of iron/artillery barrage, blitzkrieg/street fighting, than better sel that gen and create new one. Sure, blitz and tide is for tank gen and barage and street for art gen. Supply can be swithced to ace forces but not recommended. In which sequence to upgrade: just upgrade next cheapest available until you have 1 movement, 3 tank/art stars all lv3 skills and 170 hp. If you upgraded ability stars too high, for example, 5 tank stars 4-5 movement stars, you will need them later... but keep in mind that for quite a long time you will have weaker gen because of that, than just count, how many medals you lose selling that gen and consider if it is worth to do. For example, I cleared all conquests, challenges and campaigns 3 golden stars with ion canon lvl 1, ECs without 5 stars anywhere and almost all skills were lv3.