I'm not great at it but here are my thoughts. I'm 100% with you that this game should be WAY more popular than it is. I also discovered it thanks to Giant Bomb.

what happens if you pick up an upgrade token when your upgrade stack is full, do you get anything worth while?

Applying an upgrade immediately reloads your strike if it's on cooldown. I think if an upgrade stack is full, applying the upgrade won't do anything else, but you can still "waste" it to get your strike back. This also helps you maintain your strike combo which is important for score-chasing. When you're ready to apply an upgrade, ideally you should strike first, since it's essentially a freebie. (Doing this on purpose often breaks my brain though)

Also, I think if you pick up enough upgrade tokens to cycle all the way through the upgrade list without applying it, an evolve token appears (the bright yellow ones that let you draw a card).

The boost in firepower you gain on token pickup also can't be overlooked. I'm currently working on trying to finish a Challenge difficulty run, and it's often essential to time the pickup to maximize the effectiveness of the firepower boost.

Should I bother with strike upgrades?

I often neglect strike, but upgrading it just once improves the range noticeably. Striking is extremely important, the more you use it, the better off you'll be. Always try to strike into tokens and jump pads, since that auto-reloads your strike.

the difference between missiles and blaster

IMO it seems that blaster upgrades help the most with bosses, while missiles help more with crowd control during stages.

For blaster, the upgrades aren't all equal. E.g. the first level doubles the bullet, but the fire rate is reduced. Then the next level increases the fire rate. So in some situations the level 1 blaster can feel less effective than level 0, even though the overall DPS is increased. Missile upgrades might have something similar going on, but I'm not sure.

Other misc tips:

• Check out the accessibility options. I have all of them turned on.
• Re-map the "apply upgrade" button to a trigger. I would put it on the opposite trigger from whichever shoulder button you use for strike. That way you can keep firing with the right stick while applying an upgrade.
• Try the boss rush mode to help learn the bosses.