Well, for starters, we no longer use Mist to craft our weapons; Orbs of Alchemy are what we use now (but they hardly drop, so you end up purchasing them from the AH or the Depot).

Also, we can explore the Clockworks for free, as OOO has removed the Tier 1-3 fees requirement. In exchange, we rely on the Forge (and Fire Crystals, which you get from Treasure Boxes) for leveling up our equipment i.e. your equipment can't go from Level 1 to Level 4 after completing a Clockworks level, despite you having collected a large amount of heat (it just goes from the beginning of Level 1 to the end of Level 1, after which you need to use the right level of relevant Fire Crystals to 'forge' your equipment to Level 2).

While forging your equipment, you can choose the probability of being able to level up your equipment (there are 3, in which the 1st has the lowest chance of success at 30%, the second has a 60% rate of success while the 3rd gives 100% success). These 3 rates of success also give you a chance of getting some extra perks, such as bonus heat and the chance of getting a prize box i.e. the more crystals you use, the more likely that you'll obtain the extra perks (though the extras are not guaranteed, even at 100%). Hence, most players (if I'm not mistaken) would choose the 60% rate of success.

The higher the level of your equipment, the more crystals you need to raise them to the next level i.e. roughly 3 crystals to forge a 2 star item from level 1 to 2 and so on.

Other than that, you can choose the level of difficulty of the Clockworks level or Missions (Normal, Advanced, Elite). The higher the difficulty, the more risk you face and the more rewards you reap. By the way, Advanced was the default difficulty setting BEFORE they added Normal and ELite.

The amount of Radiant Fire Crystals (the crystals for leveling up 5-star equipment) now have a reduced drop rate, whereby you need to head Depth 26 and beyond, Shadow Lairs and so on to even find and obtain them. Hence, the veterans recommend keeping your weapons at 4 star, level 10 (which is stronger than 5 star equipment at level 1) until you obtain enough Radiant Fire Crystals to level up your 5 star equipment to level 5 (the exceptions to this rule are helmets and armor which grant higher protection at 5 star; do ask for more advice on specific weapons/armor/helmets before crafting to 5 star though).

Also, the Gunner update (which promises improvements to existing guns as well as new variants of existing guns and new armor) will be coming out soon (how soon is a matter of debate, though. Some say it will take a month, but you never know...).

Oh, and we now have Battle Sprites! We currently have 3 variants: Drakon (mostly offensive-based), Seraphynx (offensive and defensive) and Maskeraith (debuff and stealth type attacks). You feed them minerals or materials for them to level up, and the maximum level is 100.

If you're confused by the above, just head over to the Spiral Knights wiki for a clearer explanation (and more details). Take care and have fun!