The second thing is picking up the Healer block. I know you cannot pick it up. You couldn't do that since they were implemented. However, I think there should be a config option to enable picking up healers or picking them up with silk touch.
The final thing is Pokemon size. I've seen a huge Todadile spawn right next to a tiny tiny Feraligator. This is one of the things absolutely bonkers with Pixelmon. Yes, I agree size should have a bit of variation, but this is getting out of hand, people! Once again, I suggest a config option. Kinda like this:
//All of the following options must be either true or false. If one is true, all other must be false.
Enable Pixelmon Sizes=true/false //true by defaule
Enable only alternative sizes=true/false //false by default (only small, ordinary, and huge.