I take it I basically shouldn't be spending certs on things unless they cost 1000. The idea being that these things, being so expensive, are ostensibly the "best" things (or at least the most useful or with the most bells and whistles). Examples include the skyguard for the lightning, dalton gun for the lib, vulcan for the prowler, rocket pods, the AT/AA launcher for TR, dual bursters, etc. Exceptions include low-end infantry/suit upgrades, such as health, armor, max's offhand weapon, etc. Is this logical?
Largely, no. Few 1000 cert buys are essential or even all that worthwhile. Many open up new play styles while others are simply preference choices, but you can get by without most of them quite handily. All the ones you list offer new options to play with, but you are only likely to use each of them a few times a week unless you commit hard to that playstyle. Other upgrades are less sexy but will see use every hour in casual play.
As a rule I'd say upgrade the class/vehicle before buying new toys
unless you need the toy to make the class viable. For example, I don't snipe so held off on most infiltrator upgrades till I owned an SMG. Some people build their lightning completely around the Skyguard.
I'd say the best bang for your certs are the mid range or cheaper top end upgrades.
Buying either a regen kit (30 certs) or preferably the medi kit (50 certs) lets you equip it on any class not carrying another utility item (usually an explosive). Worth grabbing early. Treat as an extra life when you barely escape an engagement, or as a win button when you and an opponent have traded but not killed and you want to re-engage after healing.
Similarly buy a suppressor for the default pistol. 100 certs and now every class has a silenced weapon they can use to execute enemies without showing up on the mini-map.
Every vehicle weapon has a 1 cert point zoom scope and 1 cert point ammo capacity upgrade. Buy them and equip them on everything. A 1.25x zoom and few extra rounds can make a world of difference if things get hot. On any vehicles you use a lot buy the 1.5x zoom for 50 certs and as many ammo capacity upgrades as you can. 91 certs, rank 4, +40% capacity is a nice sweet spot.
Nanoweave/flak armour 4 on any given class is 211 certs. The max level is 1k certs on top of that, but rank 4 gives you a nice survivability boost. Remember nanoweave is changing soon but is going to be refunded when it happens.
Broken down by class...
Medic;
Medical Applicator (medic gun, AKA best cert source as infantry) is 690 to max (worth it), but rank 4 only 190 total and Nano-Regen Device (AOE/self heal) is only 291 total, 200 in the last rank. While it may seem a support build, it's one of the most dominant solo classes out there. Infinite, rapidly regenerating self heal? The option to quickly and safely (thanks to extended range) revive a meat shield to distract enemies? Throw on nanoweave and grab a fun gun and you are laughing. TR medics are particularly nasty.
Engineer;
Nano Armour Kit (repair gun) is roughly equivalent to the medic's applicator, but less essential to max out as you don't gain range/revive health. I'd say grab rank 4 if you ever play engineer, take rank 5 when you spend a lot of time driving/MAX-sitting. The ammo pack is oddly expensive to upgrade, but worthwhile. You get a boosted range for rank 3 onwards, letting you feed ammo to more and more people while overriding other people's own packs. I'd say invest the 160 certs for that, maybe 150 to boost it to 5m range and 4min duration. Sticky grenades and the mines (especially tank mines) are well worthwhile and pretty cheap.
Light assault;
Jump jets are frankly worth maxing out. 810 certs total, 500 in the final upgrade. You are looking at a substantial fuel increase, letting you reach higher and use the jets more often. This is a huge advantage when playing rooftop tag in biolabs. I maxed this after being frustrated by not keeping up too often. C4 is great value even if seemingly expensive.
Heavy assault;
Upgrade the nano-mesh generator to at least rank 3 for 31 certs. Only a 10% regen boost, but that's not nothing and it's cheap. Concussion grenades are a must if you ever want to use HA to melt a room of infantry/MAXes.
Infiltrator;
Recon Detect Device is worth upgrading. Recently got a buff and is seeing a lot more use. The lower ranks aren't great compared to the higher, but they are still worth grabbing at 30/50 for 2/3. Similarly upgrading your cloak makes a lot of sense, especially the 10 certs for 10% regen rate. If you plan on playing much infiltrator then go to at least rank 5 at 310 certs total. No real reason not to buy the improved hacking speed either. Anti-Personnel Mines are a good buy as well.
On another note, I feel playing TR is almost a bit of interface screw. Objects in the minimap are colored according to faction, but in the game view they're colored only by friend/foe - which means TR's stuff looks like it belongs to NC stuff because it's blue, while NC's stuff is red because they're an enemy. It took me a while to realize this was why I kept getting turned around while looking for terminals and points of interest.
You can change the colours used in the menu. I have mine set to faction colours for everything. Keeps it simple. I have also changed my platoon colours to more obvious and distinct ones (can be done by clicking on the Alpha/Bravo/Charlie/Delta squad label in the platoon screen when that squad exists). Used to be I shot a lot of Charlie members...