My first guide so bear with me. This is based off of using Ares for your first playthrough.
Certain upgrades will definitely make some levels/bosses easier. I would get stuck on Sentinel or Prime Guardian and play back through the previous levels for scrap to buy upgrades and by the time I worked my way back up to those bosses I'd have plenty of scrap to buy upgrades that would make the boss fights easier (vertical and horizontal dash ones, in particular, the weapon upgrades too).
DigiLuigi has a good upgrades guide, all credit goes to him, shows all the datacubes too:
I would suggest not bothering with the default weapon at first unless you're really struggling. Upgrade the Laser Reactor as soon as possible. Then I would do Blazing Fist (if you have the opportunity to upgrade this before you get the upgrade for the laser reactor, do it), Dash, and Air Boost at least to level 2. Go back to level 1 and get the upgrade for the prototype suit after you get it. I would then move to maxing out the wave blaster as soon as you can. Getting Extra Protection is optional as far as I'm concerned, wasn't that helpful for me. I also didn't use Solar Strike a lot. Plasma Shock upgrades aren't crucial but I found them pretty helpful as the large radius disables robots and makes for easy kills, can help a lot when there are many enemies on screen. I would save Repair, Zytron Blaster, Solar Strike, and Extra Protection for last after you've upgraded Photon Launcher to tier 3. You shouldn't need repair your first playthrough anyways to get the Unlimited Power Achievement. However, if you're struggling, upgrade Repair if you need to.
Upgrade these first in this order...
Only upgrade these first two before level 3 if you can afford to:
Blazing Fist 2
Laser Reactor 2
Air Boost 2
Go back to level 1
Laser Reactor 3
Prototype Suit 2
Plasma Shock 2(if you like, I found it to be very useful)
It'll be awhile before you get any new upgrades (level 5)
Wave Emitter 2
Plasma Shock 3 (optional)
Wave Emitter 3
Blazing Fist 3
Photon Launcher 2
Basically you'll want to clean up upgrading any of the preceding upgrades to tier 3 while playing through and acquiring previously unreachable upgrade chips and upgrading Photon Launcher 3 and Prototype Suit 3(I would recommend loading up chapter 6 & 7 to get the chips and then backing out before officially starting 2nd playthrough).
By the end of your second playthrough you should have everything you need to go for the boss perfection achievements, S ranks for you level 6. I did most of this off memory, but I will correct any mistakes I find and I'm pretty confident I did things in the aforementioned order. If you downvote please state why so I can make this a better guide!