1. Can the protocol be changed? What if changing the protocol solves the above 3 problems which are limiting bitcoin as a currency for regular transactions?
Transaction wait time & fees? On theory it's possible by reduce block time and increase block size.
Carbon footprint? No, unless proof of work (PoW) is replaced with something else.
However all of them need hard fork where Bitcoin community must agree with the changes and,
1. Reduce block time significantly change Bitcoin economy (
https://en.bitcoin.it/wiki/Controlled_supply)
2. Block size limit is controversial topic due to various pros and cons
3. Switching from proof of work (PoW) possibly violate principle of Bitcoin (
https://en.bitcoin.it/wiki/Principles_of_Bitcoin)
2. If you have a limited number of networks say 10,000 to process a transaction this should reduce transaction time? And/or how many miners does it usually take to process a transaction? Not every miner right?

That's not how Bitcoin works, you can't limit total miner or user who join the network. Average transaction time to get a confirmation are influenced by,
1. Block size
2. Block time
3. How many transaction is created by bitcoin user