Yes this is an issue i am seeing as well.
Basically all new messages will be seen in your iPhone inbox for GMail...
this includes
*sent messages
*messages that are filtered out of the GMail inbox
This is really annoying, because i subscribe to some of those heavy volume email discussion groups that i keep out of my inbox with filters in GMail... but on the iPhone.. i see them all.
If this was mac or PC, i would suggest using the excellent freePOPs program as a go between.
http://www.freepops.org/en/
for more email on the GMail FreePOPs module:
http://www.freepops.org/en/viewplugin.php?plugin=gmail
I suggest Mac engineers take a look at the GMail features for freePOPs and duplicate them in the iPhone Mail app, or just check out my list below...
these are changes that really need to be made to make the iPhone mail experience a good one for GMail users
*archive messages in gmail when they are deleted on iPhone [perhaps even change "Delete" text to "Archive" for GMail
*ability to only download mail that is in the GMail inbox
*ability to only download mail that is labeled with a specific label
*if you are looking at only a specific GMail label, the option to choose from Delete, Archive, or Remove Label [instead of just Delete]. This would be a setting that could be set for that particular mail account.
So if i have a Friends&Fam label, and i have that label set to sync as a Mail account on iPhone, i could set it to when i swipe my finger across to delete, a box comes up that says "Remove Label". This deletes the message from the iPhone, and removes the label on gmail
*when a message is read on iPhone, GMail's copy of the message should be changed to reflect it
---
While I would love to see these things addressed... i think in the meantime, I'm going to set up a new mail account somewhere. I will use it only for iPhone, and set gmail to forward certain messages to that iPhone address. Disadvantage here is, you have to archive or whatever those same messages once you log in to GMail.... hmm.
MacBook Mac OS X (10.4.10)