What makes a communication architecture/protocol faster than others?
But how can a protocol/architecture enable faster data transfer?


I am unsure what you mean. A protocol change should not make much of a difference in datarate unless you're switching from a very inefficient protocol (for example, repeating every bit 4 times) to a more efficient one.

You forgot to mention Bandwidth. An oldfashioned serial connection is quite slow (up to 115200 bits/second) by today's standards as it has a very low bandwith due to the electronics, wires and connectors that are used.

Thunderbolt is much faster not only because it uses more connections in parallel but those connections need to have a high bandwidth. You cannot use the same type of wire  that would suffice for the 115200 bits/second serial connection. For Thunderbolt you need high bandwidth (a couple of GHz) capable wire that has shielding even though differential signalling is used. Obviously high speed electronics are needed as well. Also the signal lines need to be properly terminated with the correct impedance at each end.

All that isn't needed for a slow serial connection.

I am sure I can make a slow serial connection work over a couple of meters distance using almost any piece of wire that you give me. To make a working Thunderbolt connection over a couple of meters distance you need a suitable Thunderbolt compatible cable, little else will work.