Of course there are varying levels of intelligence among different dogs, but when there are problems like you have described, the issue is usually not related to intelligence. Small breed/toy breed dogs, are generally more challenging to train than larger dogs, especially when it comes to potty training. With regard to potty training, the best method to train the dog is crate training. Whenever you are not home, eating dinner, watching TV, on the telephone, or any other time you cannot closely monitor the dog, he should be in the crate. Dogs by nature will do everything in their power to not void where they have to lay. The key is that the crate shold be large enough for the dog to turn around in, but not so large that he can void on one end, and lay on the other.
When he is out of the crate, he needs to be closely supervised, as the best way to teach the puppy that it is bad to go in the house is to catch him in the act. Bringing to the mess and scolding after the fact is useless.
If you find the puppy postures to go in the house, yell a loud "NO!", with a loud clap of your hands to startle him. Scoop him up immediately and run him outside to finish. Congratulate him and praise him when he goes outside.
As far as not coming when called, that is a behavioral issue that that you may not be able to resolve without help. As I stated earlier, since little dogs tend to be more resistant to training, a good professional dog trainer can is often necessary to help your cause. He needs consistent on leash training, ASAP. Your vet should have a list of trainers he recommends to help you.
Not chasing the toys is not really a sign of lack of obedience or intelligence. The two breeds that go into your dog's make-up are not fetching dogs. It is not uncommon for them to lack interest in toys.
In summary, your puppy needs crate training and professional obedience training. Both should be implemented as soon as possible, as the older he gets, the more difficult it will be to reverse these issues.
Please feel free to visit the dog training page of my hospital's website. There are tips and links that may be helpful:
Good luck. Please let me know if I may be of any further assistance.