After you beat a boss you can come back to them, but I find them all pretty difficult the 2nd time around...I think I am near the end of the game now. Story gets better and better.
I've upgraded every weapon so far. Some weapons you can't actually upgrade, like the bubble gun. You can get chips for them, however. The upgraded grenade launcher is amazing. You can fire up close or far away, and you will never run out of ammo with it, because you will be killing so many things to replenish your ammo. The bubble gun is a good complement to it because it shoots quickly and spreads nicely.
The level 2 (tier3) machine gun is also pretty powerful, and the only tier3 weapon to get an upgrade! The energy sword is great for bosses that move around a lot, as you can be charged up and ready to get the big hit when the opportunity strikes. But once you have an upgraded grenade launcher, I think that's a better way to go.
Favorite armors so far—deep ocean takes away falling penalties and shrugs off low damage attacks—those bees, some of the spikes in the ground—pretty handy. Also the phantom armor, which has all around high stats and chances to dodge. As far as tier 2 goes, I liked the warrior because I had an energy sword then.
Giant Tree level 12 you can take on the monster horde—this is a great way to earn 20 or 30 galactic coins...so once you have a couple upgraded weapons, take it on.