I've always personally wanted to make a chart representing what Titan abilities should be upgraded on each level. So here we go. I'm not confident on some of the choices, so feel free to comment and change.
As a basic starter: Hull is always one of the first 2 upgrades for any titan on any level (as long as it is available). The next ability should be one that uses antimatter (so that it at least has an ability to use), but that rule is disregarded with the Vorastra and Coronata. As for level 2, I've always been curious as to whether upgrade weapons & antimatter, or do another ability with one of the latter (again, excluding the Vorastra and Coronata). Here lately I've been doing weapons & antimatter and have been pleased with the results.
When level 6 comes around, of course the ultimate ability is the first pick, but after that I've always hesitated on what to do next: primarily whether to upgrade weapons or antimatter. Usually I just go by feel of the game and by what abilities I have previously upgraded.
Once the titan gets past level 6, it pretty much doesn't matter what you upgrade, because the game is probably over with by that point.
Level: 1 2 3 4 5 6 7 8 9 10
Ankylon: Disruption Matrix X X X
Furious Defense
Group Shield
Inspire and Impair X
(Hull) Fortified Superstructure X X X
(Weapons) Superior Gunnery X X X
(Antimatter) Antimatter Funneling X X
Ragnarov: Scattershot X X X
Snipe
Explosive Shot
Overcharge X
(Hull) High-Stress Alloys X X X
(Weapons) Composite Mounts X X X
(Antimatter) Magnetic Containment X X
Coronata: Subjugation
Suppression Aura X X X
Unity Mass X X
Repossession X
(Hull) Psi-Reactive Armor X X X
(Weapons) Adaptive Weapons X X X
(Antimatter) Psi-Containment
Eradica: Purification
Chastic Burst X X X
Strength of the Fallen
Unyielding Will X
(Hull) Unity Armor X X X
(Weapons) Energy Manipulation X X X
(Antimatter) Reactive Containment X X
Vorastra: Micro Phase Jump X X
Desperation X X X
Deploy Phase Stabilizer
The Maw X
(Hull) **** X X X
(Weapons) **** X X X
(Antimatter) ****
Kultorask: Nano Leech X X X
Nano Remit
Gravity Pulse
Dissever X
(Hull) **** X X X
(Weapons) **** X X X
(Antimatter) **** X X
I probably should have just made a table in word or something, but hopefully this will work too.