Could you give some specifics about the differences in your thinking? I've noticed the same thing, but most of it turns out to be "is this a job I need to do at the Mac, or can I do it on the iPad?" For manipulating single tasks, the iPad is often comparable (though there are some significant holes in its functionality), even better at a few (editing dates), but tasks involving manipulating many actions, duplicating projects, and so on make it quite apparent that while the desktop version may not look as polished, you don't have to look at it for nearly as long!
I think the iPad app looks quite nice (and compared to the other Omni apps, I think it arguably is the best) and I enjoy using it, make no mistake! Probably 80% of the time i spend in OmniFocus is with the iPad version. Unfortunately, as much as I would like to be completely free to do all my work with it, there is still too much that is either impractical or impossible. That's not a show-stopper for me, as I've at least got the option of doing it on the Mac right now, unlike the folks who only have iOS versions. I would rather see them reducing the functionality gap by bringing missing functionality to the iPad than by watering down the Mac while making it more like the iPad. Even if I had all the tools on the iPad, looking at big projects and contexts is easier with a big screen, so my target is not to actually do all of my work on the iPad.
I have no problem with a better-looking Mac version that still delivers all of the power of the current version. I'm just not willing to take it for granted that we'll get one! OmniPlan got a new major release, complete with new outlining code, after they had the experience of bringing at least three apps to the iPad. Functionally, I like OmniPlan, but I think the plans I've done in Merlin look much better than in OmniPlan 2. Unless you think the bar was lower for OmniPlan 2 because they didn't have a snazzy app on the iPad to improve upon, does the look of OmniPlan 2 make you confident that the same company is going to turn out a stunning looker for OmniFocus 2? I would be happy to be proven wrong about this, especially if I get the float on the wager until it ships :-)