Thank you for not repeating the same thing over and over and over again.
I think that the reason R* chose Johnny is because they didn't like the 'American Biker' theme. This is probably why they spit on his character and made T stomp him to death.
Another reason is that they want to prove that Trevor is a badass and for shock value but, I think it would've been better if they put Luis instead, I mean seriously, nobody likes Luis anyway.
I don't know, but I don't think that they didn't like Johnny and the Lost. In fact, I'd say that TLaD was more of a "their" game than TBoGT or even V. After IV's release, everyone was complaining about IV being too dark, story-driven, serious and "realistic". And what did they do? Made a game that was even darker and more serious and story-driven.
TLaD, in my opinion, was a game they really wanted to make and a story they wanted to tell, and that's what makes it so great. In some parts of V and especially TBoGT, I had a feeling they were trying way too hard to please everyone, betraying their original vision and what they, themselves wanted those games to be. And no, this isn't about those games being "lighter and softer".
Anyway, I have no idea what were R* thinking when they came up with the end of TLaD's cast. But my money is on shock value, and Johnny was the easiest target. Niko or Luis? No reason for them to be hanging around Blaine County and dealing with Trevor. Johnny's death served both purposes - the "Holy sh*t, Trevor just killed an old protagonist!" moment and set up a conflict between the Lost and TPE. The only other protagonist I can think of that could somehow, under different circumstances, replace Johnny would be Huang Lee, but he doesn't have the same marketability as Johnny, with him being a spin-off protagonist and all.
In the end, I was pretty shocked and pissed off about Johnny's death too at first. He was my favorite protagonist. But now, with several months to think this over, I'm quite okay with it. He didn't deserve to end this way, but his downfall made sense and, in my opinion, it didn't cheapen TLaD's excellent story. It just made it more tragic.