If you don't want the hassle of trying to find parking or ride the trolley, then I'd stay definitely stay downtown. Downtown has easy access to places like the Gaslamp Quarter, Horton Plaza, Seaport Village, the USS Midway and the Harbor. That would be my first choice.
The SD Marriott Gaslamp Quarter is just as close as the Omni Hotel is to Petco Park. The only difference is that the Marriott doesn't have a connecting bridge to the ballpark like the Omni. The Manchester Hyatt and another Marriott (SD Hotel and Marina) are across the street and down the block from Petco Park. These hotels are next to the Convention Center and Seaport Village and are also within walking distance to Petco Park.
If you have your heart set on staying in Mission Valley, you might want to consider taking the Trolley. Parking prices near the ballpark range from $15-$20, if I remember correctly but there are free parking areas at the Fashion Valley station and the Old Town station, both located in Mission Valley. There is also a Doubletree Hotel in Mission Valley which has a trolley station right next to it so you wouldn't have to drive.
HTH!