Not only colossus. Templar without storm, zealot without charge, carrier without catapult. Only sentry and stalker function ok without their associated upgrades. However, those upgrades are very good, and are part of the unit design, which completely change the ways the units is used.
However, there are some upgrades that need revamps. Warp prism speed is useless. Warp prism is useless in general. I only get to use it in heavy late game, when my proxy pylons near potential 3-rd and 4-th expo get scouted. There are no solid builds that rely on warp prism in protoss arsenal. Gateway units are weak, and if you ever get a robo, you will want to be building immortals, observers or colossus. Even if you opt for a 2-way attack, warp prism take ages to get to destination, and is too fragile to hold any agression while it is assembling back to fly mode.
I'm still convinced warp prism should be in gateway (NOT warpgate), and be available with robo. That actually makes a conventional gateway be used in late game, and makes warp prism available earlier WITH robo units at the same time. Also, change upgrade to constant warp-field in fly mode that would be awsome tech, and will see sooo much usage in the game.
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