As someone who used to play Spiral Knights religiously as a young feller, I'm devastated to see the current state of the game. The average player count at any time is in the low hundreds, which is not very good. I used to love this game, and yet now it seems like it's dying out if not already dead. I feel like there are just some features in the game that are holding the game back from prospering, and coming back to life. Here are some of the things I think need to be changed, or in some cases even removed.
The Forge
(Pointless Grinding)
The game was perfectly fine before the forge existed. There was literally no reason for this to exist, other than a blatant cash grab for the developers, which I'm almost certain did not work. The amount of profit they lost from people who probably gave up on the game after this was added is probably higher than what they got in return. I just feel like this adds an unnecessary level of grinding that wasn't present before it existed, and it didn't need to exist.
Bound Items
(Bad for Economy)
Do items really need to be untradeable? Why is every orb of alchemy you find in the clockworks automatically untradeable? This doesn't make much sense, and is probably one of the biggest things actively damaging the economy. If these items were not bound, there would be a huge amount of people selling them at the auction house, which would boost the economy a lot. This would most likely decrease the price of these items, which I'd say is a good change, because the prices can get pretty crazy. A single Eternal Orb is like 27k crowns in the auction house, meaning you need 81k crowns worth of orbs alone to craft an item. That's way too high. Making them unbound would allow them to reach a more reasonable price in the auction house, which would be a good change for everyone. And that's just one item, too. This would help make many more items accessible to everyone.
In an MMO, there's a lot of gears turning that need to be in effect. In MMOs, you need a reason to keep logging on, and when there's not a constant stream of new levels, the second best thing is making players invest and take time in their gear. Spiral Knights has always been about gear and using it to tackle challenges, so it's no surprise they've doubled down on the gear side of things.
The forge was not a cash grab, it was a replacement for mist energy and paid elevators. In the past, we could only run 10 free clockworks depths daily. While this did keep the game's economy in check, it severely limited playtime. In the days of mist, I could hardly convince any friends to play the game with me who I didn't meet in-game. Post-mist, I can casually suggest the game and get a party of friends together relatively quickly.
From a game-design standpoint, the forge is a positive. Heat used to be useless, and leveling gear didn't feel like anything proper. You would play, your gear would heat, and then it would be level 10. It basically was unnecessary and all that you focused on was crafting gear - heating was ignored. Enter the forge, where every single level for your gear matters. Emphasis put on the gear and its levels is a great direction for a game focused on gear, however I will say that fire crystal acquisition is annoying and could be altered so that players don't feel constricted.
Basically, The Forge's update brought back many older players (those who were turned off by mist especially) and kept many others around. The system is more typical of an MMO, but at least it isn't "mobile game regenerating stamina" that prevents people from playing the game at all.
Bound items are perfectly fine as well. However, from your post, you seem to mostly be upset that rarities are bound upon acquisition in the clockworks. This is because rarities are the new XP or progress bar for players. You played the game, you got the rarities, and as you play you get more.
I like the orbs being bound because otherwise, rarities on the supply depot would be absolutely worthless. Old crafting costs equal the current orb costs on the supply depot, and as someone with over 850 eternal orbs of alchemy, I could likely single-handedly crash the eternal orb market.
However, despite all of these changes being good for game design, there is an enormous flaw in them. That flaw is that the more you play the more rarities you get that you simply cannot use. I have over 100,000 shining fire crystals, and as mentioned, over 850 eternal orbs. I simply cannot use all of those, however selling them would absolutely tank their price as no-one else needs that many either.
As such, I believe a proper resolution to all issues with rarities is to allow for players to work with each other for "group crafting" and "group heating". This would be a table or area where multiple players can pool their resources, bound or not, to assist another player. Players can input items they want to use, give items to other players, and more in this way. The only downside is it uses more resources overall.
For example, let's say I'm helping someone heat a 4* item from 9 to 10. That normally would take 69 shining fire crystals for a 100% option. However, since these are my crystals (bound to me), I can use this table to spend 115 of my crystals (a 66% increase in resources). I have an abundance I cannot use, so I can cover the entirety of it, but what if it's a team of 4 who don't have 69 fire crystals individually?
Well, they could each pitch in 28 shinings and then the person upgrading the gear piece would use an extra 3 crystals. Bam, upgraded gear piece.
The same could apply to crafting. Instead of 3 orbs, you'd need 5, but since that means as a team you collectively only have to find 1 orb each with someone else finding 2, the search may actually be shorter, and the game would be more enjoyable since you're spending more time running what you want rather than grinding what you need. Materials you'd need more of, but with instanced materials again, more people have more things. You can also share recipes in this way, meaning if you are having trouble finding a recipe you can always ask someone to help you group craft and supply the recipe for you.
Lastly you could use this as a "group trading" initiative as well. You cannot trade bound items to others, but you can use bound items for crafting things (the item would still be bound to the person who put it up if it's an item being heated/crafted). This is a way to pay someone for the items they're giving you, as well as move money around for people to use for the crafting of an item in general.
This would retain the purpose of the forge and bound items, but also introduce an element of teamwork into progression in the game that is severely lacking.