I have to say it's nice to see an idea thread about Garen that doesn't try to make him a mechanically intensive champion. That said there is a lot here that I'm not a fan of.
Firstly the passive change. I like the idea of gaining tenacity, even if tenacity immune CC is very popular right now, because I as a very biased Garen main think Garen is a little too easy to kite at times right now. That said unless we are willing to remove Garen from the Juggernaut class and put him into Diver (I'm not opposed to this idea) he needs to have some sort of sustain. All Juggernauts have sustain, and while it doesn't have to be tied to his passive if Garen is to remain a Juggernaut he need to have sustain somewhere in his kit.
The Q I don't think is necessary as an anti-tank measure. Garen with his E already does very well against popular tanks. Q is Garen's utility move and helps him deal with opponents who do not want to go toe to toe with him. If Silence must be removed I would rather see a focus on the movement speed than the damage, or maybe even replace Silence with Grounded. Tanks generally sit there and take damage, making E better for facing them, so Q should be focused on those mobile squishy targets.
W I definitely agree on. It's honestly his best ability.
I don't dislike your idea for E, but it would need some serious changes to damage numbers and cooldown to fit. A lot of Garen's power budget is in his current E, and part of it's counterplay is having the damage drawn out, so that there is more of a chance some of it's damage will miss. The charge up definitely helps there, but might make it even harder for Garen to deal with those mobile opponents without something to keep them in place. Garen also uses E as a great early farming tool, with it's instant damage tick helping to get minions that he would otherwise miss. That charge up time changes that completely. Again I don't dislike this idea, it would be strong in the times where it can be used effectively, there's just nothing about it that makes me excited for it.
There is only one thing I can say about your R idea; YES PLEASE! I've always felt the Villain passive was more than a little meh. It can feel great when the Villain is a target that I need to take out first, but when it is anyone else it is all but wasted. It's either incredibly useful for my team or might as well not exist at all, and that is incredibly frustrating.
Your R idea is exactly what I would hope for from a Villain replacement. It's not tied to a particular enemy and gives me a reason to not charge in and try to take someone down. Garen has no CC so he's not great at peeling, but getting a damage boost based on allies that require his help, or require a bit of vengeance, would give Garen a bit of help in that department without moving him too far out of Juggernaut territory.
All in all this is a Garen rework thread that I actually enjoyed reading and thinking about. I don't agree with all of your ideas, but you managed to come up with new things that actually fit with the current gameplay that Garen players come to expect from him. You didn't try to turn him into a new champion, and for that you have my thanks.