From a story perspective, I'd go with the first two. Brotherhood started getting lazy with the writing, but from a gameplay perspective it's probably the best the series has to offer. It has a VR training simulator, similar to the kind of shit that you see in MGS, but the problem is that it's woefully underdeveloped. You get like 3 parkour, stealth and combat scenarios, and because the combat is quite simple, they're very easy to complete. It had potential to be the best game, if only they had developed a more robust VR training catalog.
Brotherhood introduced the "streak-kill", which is basically an instant kill that you execute by killing a single enemy, then directing your character to the nearest enemy in your vicinity and killing him. You start a 'killstreak' that the enemies then try to interrupt by grabbing you, throwing sand at your face, and varying up their attack timing. The main character has a few different weapons, and each one has its own parry timing, so you have to learn how to use them to effectiveness. It's still simple as all hell, though, like a much worse version of Arkham combat.
Brotherhood still had a number of assassination contracts that played out like a story-centric side quest. Basically, you'd take a contract and locate the target, who was usually an infamous cutthroat or criminal type, and you'd have to chase them through an obstacle course styled area that culminated in their deaths. It was good because the chase sequence incorporated the climbing mechanics.
On top of this, Brotherhood still had "Assassin Tombs", which were Prince of Persia style obstacle courses that were built inside of ancient structures, it still had the Subject 16 puzzles, which were brain teasers that revealed some implications about the origin of the Ones Who Came Before, and it had the DaVinci missions, which were side quests that involved going to a region outside of Italy and destroying a contraption that was made by Leonardo DaVinci and employed by Rome's military under the order or Alexander VI.
Every game after Brotherhood began removing features, adding useless features, and throwing in the shittiest writing you can imagine. III, IV, and Rogue use a new game engine, so they don't play the same as I, II, Brotherhood and Revelations. In short, play those games only for the Naval Combat and sailing.
