That clear lucid feeling is your brain being relieved of its addiction withdrawal. Non-smokers never have that feeling because their brain has never been exposed to it. Read Allen Carr to help you never want a cigarette again.
I think long-term smokers have a permanently-affected brain, it will be interesting to see future studies.
I have no experience with psychoactive drugs but I don't think it's anywhere as near as drastic. It's pretty easy to deal with psychologically as smoking is a lifestyle so quitting successfully mostly involves changing your lifestyle. Nicotine leaves your system completely fairly quickly with no side affects except for what I believe is a lingering sensitivity to the memory of it.
I think long-term smokers have a permanently-affected brain, it will be interesting to see future studies.