I think that you are too harsh on Jones here. It does matter that it was Rua/ an elite fighter at a way higher level than his past opponents. Yes, Rua was hurt early, but not in a way to get shut down easily. With his experience Rua was always dangerous to Jones which the latter could only neutralise by putting constant pressure on his opponent (and by quite intelligently disrupting his opponent's rhythm). Because of the pressure, from both sides, it was a very exhausting fight for both fighters. Had Jones gone more for an early finish he really would have risked to gas and be overcome if Rua had managed to bounce back into the game.
The way Jones fought that fight was the optimum he could do with his current skills and abilities (which probably will still improve). I think he couldn't have done it otherwise without raising the risks very much. If he had lowered his pace focussing on a 5 round fight he would have left openings for Rua to imply his game and if he had looked for the finish earlier he would have risk to really gas.
So for the original question whether Jones would survive five rounds. In a fight similar to the Rua fight, without getting a TKO in Round 3, I think Jones would get into trouble in the later rounds. The constant pressure would take its toll, but Machida is not Rua. Machida's fighting style is different from Rua's. Jones wouldn't need to put the same constant pressure on Machida as he did on Rua. So if he is intelligent/cautious enough to pace himself, Jones has a very good chance of surviving five rounds with Machida.
However I also think that Machida with his fighting style could have one of the best chances to win against Jones if he can avoid major damage due to his elusiveness and bring good counters. In a pure pressure vs. pressure fight it seems that no one can compete with Jones at the moment (besides a lucky punch).
But the point is, Rua vs Jones was not a particularly fast paced fight. It was tactically hard for both of them, but it was not a body tester. Rua got hit hard early, was on the bottom, and was fighting a much bigger man, so him running out of steam is explainable without even mentioning his surgery etc. If Rua could have bounced back into the game he would have, it's only his physical toughness, ground defense, and Jon tiring that let it go on for longer. Rua would not have bounced back if Jon went in for the kill earlier, it would have been too much.
Jones took much less damage, was always in advantageous positions on the ground, and could throw strikes well out of Rua's range, but by the start of round 2 he was noticeably tired. That is not just down to pressure, he doesn't have a fantastic gas tank right now and he is a big man. He's bigger than many HW's, there's a reason they don't bother cutting to 205.
I've said it before and I'm calling it now, it doesn't matter what type of fight Jones is in, who he is fighting or how much pressure is involved, he will have cardio problems past round 2 and it will be because he is in the wrong weight division. You can say Jon did the smart thing by not trying to finish Shogun earlier, but Shogun was rocked, tired, and wasn't presenting any solid offense. To me that means Jones either doesn't have killer instinct, or was too tired for no good reason, and I don't think he lacks killer instinct.
I'm just not impressed by this monster cutting weight, steamrolling smaller and more skilled guys but maybe knowing that he is not as fit as he could be. To me that is an incomplete fighter taking advantage of his youth and size, I'd rather see him put on some mass, fight bigger guys and know that he can compete with them in terms of fitness, it's not like he would lose his reach advantage[the deciding factor in his LHW fights] he just wouldn't be able to rely on it so much and he'd probably be healthier.