This is an important topic to address, Bistro. I'm glad you are looking into it.
I agree that the Wilderness is dead for the most part and is near impossible to revive at this point. However, rather than looking at solutions to fix the problem, I think it's more important to focus on what "killed" the Wilderness.
Although you mention Bounty Hunter and Clan Wars as being a major culprit, Bistro, I think the removal of free trade played the biggest part. The fact of the matter is that people didn't PvP just to PvP (at least not to my knowledge). Most people did it to make money. Now I'm not saying these people didn't enjoy PvPing, they most certainly did. But it was the fact that they could make money off doing something they enjoy (which is really a major component to RPGs as a whole and absolutely true of Runescape) that made PvP in the Wilderness popular and viable. By taking away unlimited drops and restricting PvP to select areas, it made the Wilderness a boring place.
Once Jagex decided that the Wilderness should be brought back (and trust me, it was Jagex's decision, not the players), by that point too much time had passed. The game had moved forward while the Wilderness remained a bleak and pointless part of the Runescape landscape. The majority of the PvP community had either left the game or moved on to other parts of the game. This created a major problem as 1) the interest in PvPing in the Wilderness was gone and 2) even if one wanted to PvP, no one knew how to do this anymore if they had not kept in practice. With the changes to combat a little later on, this became the final nail in the coffin for the Wilderness. There was simply not enough time to rekindle interest in Wilderness PvPing at this point. With a whole new combat system and new equipment, all bets were off and it left people scratching their heads as to "What the hell happened here?"
In summary, the Wilderness was killed off by a desire to fix the issues bots brought to the game. In order to fix one problem, Jagex sacrificed the Wilderness and the PvP community without considering the long term consequences. Although I can't speak for Jagex but only conjecture, I assume that the developers thought that the PvP community would continue to live on and flourish despite the removal of the Wilderness. This turned out to be false. Over time, the PvP community died off with only the most diehard of players sticking around, but leaving hardly any notable community behind. Although people wanted the Wilderness back, the majority of these people weren't PvPers and probably just wanted the Wilderness to come back regardless of anything it may have to offer. With a new combat system and little time to adjust, any would be PvPers simply found it unfeasible to take up PvPing as there was little interest monetarily or otherwise.
If there ever was any hope to fix the Wilderness, it would be to make it a viable means of earning money in the game as opposed to many other methods. But even with this, there needs to be a concerted effort to generate interest in the Wilderness on Jagex's part. It can't just be "Oh hey, look at what there is to do in the Wildy now!" type of effort, but rather a "The Wilderness is an epic place where you can make money, have fun, and enhance your game play experience by participating." If Jagex can make the case that the Wilderness is a fun place to be, this will be how the Wilderness can be brought back to life.
RSBANDBInformer! Gaming Writer: 08/31/2011-09/30/15
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