I'd have to agree that a lot of the "anti-mecha" argument boils down to pure hypocrisy. It's not a matter of "time-traveling dragons", it's a matter of something fundamentally alien in a setting. We simply don't have giant robots in the real world, and to an annoying nuraber of people, this seems enough to damn the entire idea. It's why starfighters are so readily accepted, or "space truckers"; hell, you could even find some way to rationalize a tank in outer space and it wouldn't provoke the same knee-jerk reaction, because these are all things we have in real life...IN SPACE!
What I'm seeing is a kind of pop cultural Luddism. Giant robots are no more "impractical" than fighter jets IN SPACE!, or battleships IN SPACE!, or infantry IN SPACE!. What drives people nuts is the simple fact that they have no direct real-world analogue (yet), and unable to express this thought clearly, they encapsulate their irrational reaction in a faux-intellectual statement.
I mean, really. Jules Verne put a man on the moon with a cannon. If you suggested to him that you could put a man in a giant metal phallus packed with fuel and ignite the contraption in such a way that it would launch into orbit, he might have laughed. H. G. Wells would have looked at you strangely if you suggested his Time Traveler might find himself unable to return to the same future he left: quantum mechanics hadn't been discovered yet. Arthur C. Clarke described an office in 2001 as being fully equipped with typewriters, for crying out loud. What seems pure fantasy today may become reality tomorrow: after all, Star Trek had pocket-sized flip-top voice communication devices (cell phones) and music via computer (MP3) long before such innovations became commonplace.
With the matter of "impracticality" and "suspension of disbelief" hopefully laid to rest, let's return to the issue of "robot shows as toy commercial". Of course robot series are made to sell merchandise. It's why television shows are made in the first place. No network exec or sponsor ever looked at a series and said "hey, this is a great story, people should see this": what they say is instead "hey, this show looks like it'll sell lots of merch or advertising space, let's put it on the airwaves". It's a brutal truth that permeates all media: people don't typically make shows or write books or compose music or develop games to fulfill some grandiose artistic ideal, they do it because it pays the bills. And if that's the only reason, then yes, you end up with soulless, mass-produced crap.
But not every series, mecha or otherwise, starts with "hey, let's make a show to sell toys/advertising space". Some do indeed start with "hey, let's tell a story and try to sell it to the network", or "hey, I have this really cool idea for something no one's ever done before..." Money may provide motivation, but it's not always the initial impetus behind a story. And before you say "why can't the story be told without giant robots?", I think I've already well-explained that there are things you can do with a giant robot story that you can't in other settings. Could you write a story concerning a war spanning a fantasy continent approximately the size of Europe, set in a world at an approximately medieval-era level of technology, where the plot hinges on quick and efficient communication between factions through plausible real-world means? Of course not; you'd have to either rewrite your story or change your setting. What about a story set in a far-flung Information Age future where everything is connected through the Internet and all information is readily accessible from any terminal, yet the protagonists must race against time to find the text of a mysterious piece of folklore? Again, either change the plot or the setting. (It's worth noting that .hack actually has almost precisely that exact storyline, but its means of handwaving why "The Epitaph of Twilight" is nowhere to be found is somewhat unsatisfying.) Giant robots allow characters to remain both anonymous and yet unmistakable, they're human enough in appearance for audiences to connect with them, and they can evoke a certain kind of primal awe: you couldn't have Setsuna F. Seiei in a world without Gundams. (Imagine the sheer ridiculousness of having a character convinced that a tank or a fighter jet was the closest thing in the world to God. Talk about suspension of disbelief problems.)
A giant robot story is intrinsically a giant robot story: yes, this hearkens back to "Gundam is Gundam because it has Gundams" or however the rebuttal went, but hear me out. Giant robots offer the aforementioned storytelling opportunities, but they are also a stylistic choice that affects the entirety of the work in question: you can't change a giant robot series into a non-giant robot series any more than you can set a space opera in the Middle Ages or recast a tale set in Babylon to take place in New York City. It's possible, but things will inevitably get lost in the transition - often good things - and the end result is almost inevitably not worth the effort. Imagine someone who hates the idea of incredibly human robots in fiction: you could theoretically change Blade Runner to appeal better to this individual's worldview, but would it necessarily be better as a result?
Conversely, you can't just randomly decide to drop giant robots into a setting and expect to make a giant robot story any more than you can randomly decide to put apples in a blueberry pie and get away with calling it an apple pie. Some people might appreciate the resulting concoction nonetheless, but others would be well within their rights to say "this would've been better if you hadn't changed your mind at the last second."