What's confusing to me is that you keep saying "active sub", but the fact that you are driving the Pioneer 6.5" with the TPA-3116 means that the Pioneer must be a passive sub.
Assuming the Pioneer is a passive sub, and both are 4 ohms, and the amp really can handle 2ohms, then it should be fine to run the shaker and 6.5" Pioneer in parallel. You won't be able to balance the signals between the shaker and the sub though. You will either have mostly shaker or mostly sub depending upon which is more efficient -- unless you luck out and they happen to be balanced naturally. You will have the same issue with crossover -- where the crossover that is ideal for the sub will almost certainly be too high for the shaker. If your long term plan is only use one (sub or shaker), then it should be fine because you can tweak the settings for that one shaker or sub.