I dunno - I've loved the GTA games since GTA3. Dunno what that says about me - but I love me some GTA here. [shrug]
My favorite is definitely GTA: Vice City - for the improvements of character & story work over GTA3; the new bikes; the setting of Vice City (Miami); the improved PC performance over GTA3; the awesome 80''s soundtrack; etc etc. It just felt like VC aimed more of the period piece and art side of stuff.
But, I dunno - which is the best GTA overall? Hard for me to say. GTA: VC is great, still for all the stuff above - but, I dunno if it holds up as much on some other stuff: namely gameplay, combat, and performance. Many of the other GTA's - especially say GTA5 - just play and run much better, in all of the regards that I mentioned in the previous sentence.
I prefer GTA5 for a gameplay & performance factor. GTA5 felt like a GTA: Greatest Hits - where Michael was another Tommy Viccetti; Franklin was another CJ type of characters....and then there's Trevor, who seems to represent every GTA players that just wants to do bonkers & crazy stuff.
I still love GTA4 for the story & character stuff w/ Roman, Niko, and whatnot. Gameplay was more toned-down and realistic, compared to previous GTA's. Though, I really thought Tony DLC was fantastic and more outlandish, like older GTA's - it was less grounded and more fun, feeling like a modern VC in many ways. I really liked the biker-based Lost DLC - but that was less grounded than GTA4, but still nowhere as bonkers as say the Tony DLC.
As far as Saints Row series goes - I like them, but for me...SR: The Third was just it. When GTA was getting a bit more grounded & serious (i.e. see GTA4 base-game) - here comes this bananas game. It was like all the crazy GTA games amped up and parodying everything to a zillion...and I loved that. I like SR4 - but eh, too much rehash on the game-world and assets....though I did like a lot of the references to Mass Effect games, Matrix, Keith David, aliens, and any other non-sense & jokes they had going on. Most of the SR games since SR2 have been good, except for that Gat game.
Though, I do think one of the best GTA-type of games was Sleeping Dogs. My God, was that game awesome and underrated. Taking that GTA formula & flipping it on its heads where combat was hand-to-hand combat based and similar to Arkham's combat (at that time, wasn't burnt out w/ that combat style yet) instead of shooting-based; that Hong Kong setting; that storytelling; that awesome quality of voice-acting - that game's a gem.
I like Watch Dogs for its approach to stealth & hacking, to go right along w/ the GTA formula and UbiSoft formula (for better & for worse) - but, I dunno if it'll ever reach the insane hype it ever had. I don't know if it'll ever hit the heights of Watch Dogs 2, either. Sure, I liked WD1 and WD: Legion was cool - but those games do have some issues. It seems like...WD2 found that happy medium w/ storytelling and fun - while WD1 felt too serious, cliche, and predictable - and WD: Legion just really can be very repetitive & it lacks some story and/or character development...since you can pretty much recruit anyone.