Specialist

In place of the Support class of the first game of the reboot, Specialist is probably the most versatile class in the game. Though its main purpose is to support the team, a Specialist should not be left behind in fire power. Equip them with powerful PCS or ammunition so that they can be involved in offense. Just like in basketball, in XCOM 2 great offense beats great defense all of the time.

Assault Rifle is the primary weapon of the Specialists. The GREMLIN drone is their specialty, the drone has several utility but the greatest of them all is its hacking potential. With right amount of planning and risk-taking, you can have a formidable Specialist that can hack every mechanical unit in the game.

Specialist is the best class to carry Skulljacks because Skulljacks provide Hack stat bonus, a large sum of it!

Battle Medic vs Combat Hacker

Here is the Skill table for the Specialists.

Medical Protocol vs Combat Protocol

Right off the bat, the Medical Protocol skill trumps all over Combat Protocol. However, in terms of scalability, Combat Protocol gets powerful as you progress because of the several upgrades for the GREMLIN drone that also carries bonuses to its offensive output. Medical Protocol just drops its usefulness too quickly to be life-changing late game.

Revival Protocol vs Haywire Protocol

Personally, I do not like Revival Protocol. I do not want to put my soldiers in a situation that they are in need of revival. Instead, just go with the Haywire Protocol each and every time because once you meet a Sectopod, you'd want to hack it and flip the script. Other mechanical alien units are also worth hacking because they have lots of utility and have armor by default.

Hacking

The bonuses you can get in hacking several interest points will gain you large amount of Intel and other supplies. The mission bonuses are not worth it though, and you got to be careful with how you read them. Just remember, all of these "gain immunity for three turns" are not worth it. Pick the lesser bonus with higher chance of hacking than the greater bonus because they are always almost useless. If by chance there are bonus hacking stats in the bonus choices, cheese it! Save-Load just to get it, it is worth it. Once you get one successful Hack stat bonus, it is dumb easy to hack everything.

Field Medic vs Scanning Protocol

Field Medic is actually pretty nice to have around. You have to give up an armor, a grenade, a utility, Skulljack or an ammunition for the slot though. If you are not too keen to on giving up any of these, there is no need to choose Field Medic. It is not that Scanning Protocol is useless, however, it breaks the game for me (graphical issues), so I cannot really comment on it.

Covering Fire vs Threat Assessment

Both are fine. Choose what you like.

Ever Vigilant vs Guardian

Both are really good also, choose what you like most. Ever Vigilant is almost cheating when you want to blitz through the map, though. Guardian is also good in keeping aliens in check especially when you have PCS that provide several bonus perks or damages. Both of these skills show you that you have to invest in the offensive output of your Specialists because once you get to the the Major rank, Specialist transition into more of an offensive juggernaut more than a utility class.

Restoration vs Capacitor Discharge

Restoration is useful across every situation. By the time you reach Colonel, you probably have insane hacking skills that you do not need the Capacitor Discharge skill. Still, the latter is useful in tight places but Restoration's added bonus of not just healing OR reviving an ally but also REMOVE ALL THE NEGATIVE STATUS is mind-boggling. Men, you cannot say no to that.