I still disagree

I was gonna write up a longer post detailing why none of the various complicated aspects of Protoss are actually a problem but I figured it'll save us both time if I address all your concerns as you brought them up ^.^

In late game you are correct certain Protoss armies are considerably slower than most Terran and Zerg armies. However the cost effectiveness of Protoss units also entails that we should through proper use of High Templar/Archons/Colossus be able to deal out enough splash/aoe to make it so we don't need to take a max fight vs max fight. We can engage with warp-ins and good storms and still take a fight that we may be at a 20-30 supply disadvantage at. With proper micro, the size of a Protoss army (which is naturally smaller anyway) can easily stand up to any bio army and most zerg armies. 

Your point about mutalisks is incorrect. Mutalisks are disliked by Protoss not just because of their mobility but because of their HP buffs in HoTS dealing with mutalisk flocks is incredibly silly. They can dodge storms and regen far too quickly and Stalkers aren't cost effective, thus their only counters are slow and clunky archons, storms, or phoenix. Phoenix being the "hard count", while also suffering from the stigma that if you have max ranged phoenix attacking a flock of mutas and the mutas decide to turn on the phoenix you have .483 seconds to micro your phoenix away before the mutas start shooting them back. Protoss hate Mutas for this reason, and that due to the cost ineffectiveness of units like Stalkers versus them with the addition of their utility through speed make them a pain to deal with.

As for your remarks on creep spread it is your job as the Protoss fighting against the creep spread to be willing to take observers or oracles out and kill the creep tumors and remove zerg's vision. You may not get a pylon up, however with two speed warp prisms and the threat of an army that's limited Zerg's map vision zerg can't easily deal with your late game harass. I find in particular if you open with 1gate expand into 4 or 5 gate pressure while teching you can very easily force zerg into a situation of you having a strong advantage pressed early and keep Zerg having to play safe rather than greedy. 

Even against Swarm hosts and mutas this strategy of using your units to keep track of an enemy's location and countering works. I've played players with good and awful creep spread and in every circumstance I've walked away with an 80% Winrate vs Zerg in PvZ. If you're proactive in keeping a map presence you don't lose your options, you just have to be smart about how you play the game out.