I think the difference in the two is perhaps one is more agreeable to the new spec tyres & the other doesn't & suffers from chatter.
To me from looking at onboards it seems the Yamaha has an advantage in corner speed & the Honda has an advantage on the straights.
In my opinion for what it's worth, Honda had an advantage last year & so far Yamaha has one this year. Even the Tech 3 boys are bloody quick on that bike.
Having said that, neither Cal or Dovi are in Lorenzo's league as a rider.
To sum up, last year the Honda was the pick of the bunch but it needed a Stoner to get the championship off Lorenzo.
This year Yamaha seems to be the bike of choice but it needs a Lorenzo to ride it to win a championship.
A couple of things that have left me scratching my head this year.
Lorenzo was terrible in the rain in the lower categories. Even from pole if it rained you knew he would be going backwards pronto.
But now he is smashing everbody on damp tracks by 10 seconds in cruise mode & he could have won by more.
The other thing is the length of time it has taken Honda to get over their chatter issues. It was reported as a problem even in testing at Malaysia before the season begun but here they are at exactly the same place.
Well here is one opinion backed up with some thought (I haven't got to you Mike), ok, the tire. So this is the major factor in your opinion, that the Yamaha is a better bike than the Honda because the new tire is more agreeable to the Yamaha? And you say this year the Yamaha is better, though Honda dominated pre-season testing, so I'm not so sure. Well, Ben Spies has complained about chatter problems too. Its also believed that the factory and Sat Yamahas start out the same going into the season, yet the podiums have been dominated by Honda, fact. So, yes both Casey and Pedro have complained about the new tires, correct. Specifically, the front tire, right? Lets be clear, that the only two complaining about this tire are Casey and Pedro. The other two Honda riders have preferred the other option according to reports. Of course, Pedro said rather arrogantly, 'well look at their lap times'. This from a guy who is getting beat by his teammate most all the time. So obviously, even Pedro isn't pushing the tire like Stoner is, correct? Now in 2 events, we have only had 5 races so far, Stoner cited arm-pump and a rear tire wear issue (Qatar/Britain). In the other three events, Stoner won two (Jerez & Estoril) and, finished off the top step in horrible wet conditions in Le Mans. Stoner used the wet tires in France. So then, we can't possibly conclude the tires were the problem there right? That leaves us the Catalan GP ONLY. Here Stoner got pole! Not exactly a bad tire day, eh? Maybe those tires can handle the forces imposed on them (as Pedro suggested the contrary), surely a pole lap pushes the tire to cope with forces more than a race in a one off lap? So how did he do in the race? Off the podium. So this was when the bombshell of his retirement was the talk of the town. But wait, his teammate, the guy who said look at the other guys lap times, came 2nd that race (surely this must count for something in the tire debate). Now that I've narrowed it down to the Catalunya GP, lets take a closer look at it in terms of this issue of tires. We are talking about a battle for the hometown crowd between to Spaniards desperate to be loved by their countrymen. We knew it was gonna be a battle royale, both Spaniards putting their tires through a serious test of wits and pressure. Lorenzo came up on top while Pedro said rather uncharacteristically, he got beat, kudos to Jorge. I might have missed it, but I don't recall Pedro kicking up much fuss about the tires. And trust me, I put everything Pedro says under a microscope.
So, out of the 5 events so far, we can eliminate 4/5 in terms of tires, since one Stoner didn't even use the tires in question (rain tires), and the other two the man cited a completely different issue, and the other two he won. So we are now relegated to determine that the Yamaha is better because in the only 2 events where we could safely say the tires where the issue are Jerez and Catalunya. Casey won Jerez! That leaves us win ONE race then. If you want to base the tire woes on practice session, well, Casey has lead more. So again, I'm not confident the tire is the reason why I would say the Honda is inferior to the Yamaha other than the HRC boys have complained about it.