I don't know what level of suggestions you're looking for, but brainstorming is so much fun, and this seemed like a cool idea, so I thought I'd share it-

Two things I noticed as I was playing: First, using two digits in the level field on equipment just begs for those digits to be filled. As it stands, they only go up to level 10 (well, Proto equipment does, maybe other ones have a higher max), and then it stops dead, and it seems like a waste of potential.

The other thing that caught my eye were the modular bonuses that certain pieces of equipment get when you hit milestone levels. The Proto Gun, for instance, gets a charge speed bonus at level 5 or so, then an attack speed bonus at a later level.

What if, instead of stopping progress dead at 10, you had the option of levelling up a piece of equipment further, past its normal limit of 10 (for a fee- 150 energy or so) and every 10 levels you would gain a random bonus to the equipment's stats, in the style of those modular bonuses. The equipment wouldn't scale in power at the same rate that they do before level 10, but the bonuses would provide some extra strength out of the equipment, and allow for a degree of personalization. You may end up with a Cutter that has a chance of setting the enemy on fire, or a Swiftstrike Buckler that prevents you from being frozen. With the number of base equipments and possible bonuses, the permutations skyrocket, and you have a pretty good chance of having a piece of equipment that really is unique to you.

This system would dramatically increase the ceiling of progress in the game- not only because it would allow equipment to be leveled up 9 times further, but different combinations of random bonuses would naturally be better than others, creating a hierarchy and rarity of equipment (each permutation might not be any more likely than any other one, but different tiers of quality- how well the bonuses work together with the equipment's base stats- might be). Couple this with an option to de-bind equipement (again, with an energy cost), and an extremely high value market for players who are so dedicated will create itself.

It could even be a way of providing a reason for re-visiting lower level equipment (it seems tragic to me that there are these beautiful unique models and actions for each piece of equipment, but once you get an upgrade there really isn't any reason to see it ever again). If each piece of equipment has a natural max level- that is, the maximum level that it can achieve before you have to pay to level it higher- and stronger equipments have higher natural maxes, then they will get fewer random bonuses before they hit level 90. A shield with a natural max level of 20 will be guaranteed to have better stats at level 20, but one with a natural max of 10 has a lower guaranteed power, but a higher potential, depending on what random bonuses it gets.