Media Encoder: Slow performance

No problem. You have a few options here:

1) Instead of going straight to H.264, I recommend encoding to ProRes 422, then converting that to H.264. It's an extra step, but you can do a test yourself and see how much faster it is to encode an intermediate format like ProRes which is far less compressed than H.264.

2) The public beta of After Effects (available from the "Beta Apps" section on the left side of the Creative Cloud Desktop app now has multi-frame rendering available. You can install this alongside the shipping version of After Effects without any conflict. Currently, MFR only limited to the After Effects Render Queue, but it will be coming to AME and eventually, the Preview panel. There are caveats, as not every effect is MFR-ready just yet, but it will likely be a faster export than if MFR was disabled. I've seen exports with MFR enabled that were 2-3 times faster.

3) Find out where the heaviest part of the template is and see if you can remove unnecessary effects or reduce the amount of processing needed. Perhaps you have a super heavy blur or a particle generator and you don't need as much blur or as many particles—you can reduce those values for quicker processing.

There's lots that can be done, but in short, After Effects is a compositing application at its heart and its job is to handle lots of pixels and process them accurately, vs playing back in real-time. Good news, though, with some serious performance improvements from the last few years, along with the addition of multi-frame rendering, things are starting to change.