I've stayed at both many times!
Anaheim Plaza is definitely closer, but you can take the ART bus to the Park from Stovall's, as it picks up/drops off right in front of the hotel. You can also walk down
Disneyland Drive and take a shortcut through the Grand Californian lobby, if you want to be sure to be to the Park at opening time. It's about a 10 minute walk to the Park from Anaheim Plaza; it's about a 15 minute walk from Stovall's.
Though I've enjoyed my stays at both hotels, I'd choose Stovall's, as it's been recently renovated. Here's a picture of a room I stayed in last summer at Anaheim Plaza:
As you can see, the decor is a little outdated. However, the room was much larger than an average motel room, had a fridge and a microwave, and a balcony big enough for 2-3 people to sit out on.
Here's a picture of the room at Stovall's I stayed in last summer:
The room was average sized, but was newly refurbished. The beds were SOOOO comfortable, and there was also a fridge and a microwave in-room.
Stovall's also has topiary tree animals throughout the grounds:
The pool at the Anaheim Plaza is huge, but the pool area at Stovall's is more inviting, IMO. There are 2 hot tubs, and 2 swimming pools, one heated & one not. There's a cool round poolhouse at Stovall's, too:
The free breakfast at Stovall's wasn't anything fancy, but it was fresh & constantly restocked. There were apples, bananas, a few different kinds of dry cereals, biscuits & gravy (which were actually really good!), donuts, Danish pastries, and hardboiled eggs. The breakfast buffet at the Anaheim Plaza (not included; it was $9.99 for AYCE last time I was there) was typical Denny's/Coco's breakfast fare, but it's a great bargain as one would be lucky to get out of either of those restaurants for $9.99! The buffet had bacon, French toast, sausage, fruit, oatmeal, yogurt, scrambled eggs, croissants, pancakes, and a quite a few other breakfast foods. Again, it was nothing fancy, but it was fresh, plentiful, and affordable.
I'm not sure how much parking at the AP is, as I've never needed to park a car there. I think it was around $5 a day. Parking at Stovall's is free.
Though I've enjoyed my stays at both hotels, I'd choose Stovall's, even though it's further away and more expensive...to me, it's worth the extra $ for the updated rooms & comfy beds.