When we've used online check-in, we are greeted by name as we get off the Magical Express bus and escorted to the check in desk. It usually seems to take a bit less time (but not always).
Requests seem to be granted about the same percentage of the time no matter which check in method we use. I always make requests through MS and ignore any request fields during the online check-in process.
For me the largest advantage to online check-in, is the ability to type in my own credit card number for charging to the room and express checkout. When I use online check-in, I do not have to give my credit card to the CM at the front desk. (There have been reports of front desk CMs arrested for participating in identity theft / credit card theft). I know that is a small risk, but it is one I can eliminate.
In summary, it really doesn't matter which way you check in. (Disney prefers online check-in as it saves them time & money, LOL). It's just personal preference.