I don't know why Apple makes setting "reply to" email address so difficult (and I remembered it being much easier in earlier versions of the iOS) but it seems like Apple doesn't really want you to set this up. A typical email client will allow you to setup a different email address as a "reply-to" email address from the real email address/account, but this feature appears to be missing from the iPhone. I finally was able figure out how this can be done in a two part step. Note that this instruction involves Gmail as the email account I'm using (but I think it can be done via other email systems).
Step 1: Setup your Gmail on your iPhone as "Other"
Your iPhone email client gives you several options to setup your gmail account; most people use the native Gmail presetting or Exchange method if they want to have push-email. Here are the exact steps (must follow every step!):
1. Settings>Mail, Contacts, Calendar>Add Account
2. Choose "Other"
3. Choose "Add Mail Account"
4. Fill in "Name" (it can be anything you want)
5. Fill in "Address" (use your Gmail Email, for now)
6. Fill in "Password" (matching Gmail password)
7. Fill in "Description" (this is just a label for this email account for reference)
8. Hit "Next" and allow system to validate
9. In the next screen, iPhone will prompt you options to setup Incoming and Outgoing Mail Servers (both are required, even if it says optional, this is whats going to be referenced for later step)
10. Add Incoming Mail Server (imap.gmail.com), Add User Name (same as step 5), Add Password
11. Add Outgoing Mail Server (smtp.gmail.com), Add User Name (same as step 5), Add Password
(If you are using Google Apps to host your domain and email, you have to enable SSL and select Port 465 instead of using the Non-SSL and default port of 587)
12. Hit "Next" and if everything checks out, Hit "Save"
13. Hit Home button to take you out of the settings Men
14. Settings>Mail, Contacts, Calendar> and choose the account you just setup
15. Select the Account again to edit the settings of said account, this is where you would change the "Address" field to a different "Reply To" or "Sent From" email address you desire
16. Hit "Done" when you are done
Step 2: Enable Gmail to "Send Mail From Another Address"
This step is needed or required by Gmail to ensure that you are not just pretending to send out a bunch of emails like you are someone else (like pretending you are your boss or Bill Gates). Gmail offers a good step by step instruction here. In short, once you login to your account, go to the upper right hand corner and go to "Mail Settings". Go to the 3rd tab "Accounts and Import" and go to the 3rd section "Send mail as". Gmail would walk you through a couple of more steps to validate that you have the rights to the said email.
Once both steps are fulfilled, you should be able to respond to the email account with a different reply to email address. It's a few steps but this is the much needed missing options for the iPhone folks.