Having recently completed TLAD, I found this discussion quite interesting.
The first thing that I noticed - and had problems understanding - is people calling Johnny a rat. How is he a rat, exactly? Every time he recieved a call from the FIB, he told them to back off. Billy and Brian are the obvious rats here - Brian being your typical brainless goon who only follows the bully boss around, and Billy selling Johnny, Clay, Terry and Jim out after not being able to maintain his authority over them. But this has all been covered in simonp92's post on the first page already, he worded it far better than me.
That being said, somebody also said Johnny dragged the club down. Really?! He put the Lost on the right track while Billy was gone, focusing, as the game's manual says, "the gang’s activities on deals and truces, instead of petty vendettas and mindless violence", as Billy used to. Billy just tried to convince everyone what a "real man" he was, his pride was the most important thing in the world, he was incapable of dialogue and discussion, he shot a deadbeat in the back, breaking the truce with the AoD without even giving Johnny a chance to explain why it would be a bad freakin' idea. Nnoooo, he had to have his bike back! In short, and I'll refer to the manual again, he had "one set of priorities: bikes, booze, babes and blow; in any order and preferably all at the same time".
Billy calling Johnny his brother a gazillion times doesn't mean much, at this point the "brotherhood" and "bikers 4 lyfe lel" were starting to lose meaning, like the characters said more than once, it didn't mean anything anymore. Billy just kept talking like that because he was clinging onto the past. Also, like somebody has explained already, he used Jason's death as an opportunity for that cliche, cringy speech about them being brothers, all the while lying that it was the AoD who did it only to help himself remain leader and get others to follow his mindless orders.
The Lost couldn't have survived under his guidance, all he wanted was chaos, pointless violence and all-out war against other criminal groups. And there being several organized crime groups and mobs in LC, all larger and stronger than the Lost, the club was far more likely to survive by building business relationships rather than destroying them. Thus, Johnny was making much more smarter moves than Billy.
When it comes to Ashley, the way I understood it, Johnny finally is capable of letting her go. Near the end of the story, he finally tells her to leave him alone, even says it twice (see this). Besides this, even later on (and this might be a minor reward for getting 100%, as I only noticed it after completing the game 100%), Johnny receives an e-mail from Ashley saying that she got kicked out of rehab and needs money, to which he replies something along the lines of: "Good luck, Ashley. And don't ever speak to me again." And that's the positive reply, mind you, I still haven't tried the negative one. So Johnny being emotionally too weak to let her go is simply not true, IMO. At the end of TLAD it is implied that he finally doesn't want to have anything do with her anymore, which, along with what happens in the story and how the chapter ends, provides great closure for the whole DLC. It is only in GTA V that it is implied that he has gone back to her, and has even gotten addicted to heroin or whatever. So the way I see it, back in 2008/9 Rockstar imagined Johnny as finally getting closure and moving on, but changed their mind later on with V in favor of, like has been said already, cheap shock value and making Trevor look like a badass.
There are still some points that I would like to cover, but I'll just stop, think this is enough for one post.
I will give kudos to 1775 and others who are trying to look past what seems to be the case at first glance (e.g. trying to see Billy as the good guy, etc.), but I just think your interpretations are wrong. So no, Johnny did not deserve the ending he got in V, he deserved the ending he got in TLAD, and no, his part in "Mr. Phillips" does not feel right.