So where do we go if shutterstock, pond5, etc...  are not worth it?

You mean: Is there any secret agency nobody knows about where you can dump your stuff and get fair commissions with decent sales volume?
The harsh answer is "no".

Many, myself included, tried (or some still try) to compensate the commission cuts by adding "just another agency", but that potential is really limited.
Any additional microstock agency apart from the big three only increases your income with a few percent max.
At least, that's my experience. For images, I barely do video.

Those big three (Shutterstock, Adobe, iStock) bring in roughly 75-80% of my Microstock income. They are the market and dictate it. (or get dictated if you ask them)
The other ones like Dreamstime, BigStock, DepositPhotos, 123RF, Alamy, P5, EyeEm and so on just linger around.
All combined they struggle to make a quarter of my income and that share seems to be declining.

POD and book covers are widely discussed here, but to my feeling (not doing POD or book covers) it's roughly the same numbers game with slightly different content and again quality as decisive factor between making pocket change vs significant income. Basically the same as Microstock.

Microstock at least has the advantage that it's a very broad market, and uploading to a variety of agencies can be (partially) automated.

Also not sure how to interpret "the not worth it".
If you are not selling at Microstock in terms of volume, you probably need to up your game and provide more and better content, correctly keyworded. 
If you feel like commissions in Microstock are an insult that you aren't willing to take anymore, then it's simple: time to quit.

Or get into one of the premium and niched agencies if you have a portfolio that grants you the entrance ticket and you have the ability to consistently shoot premium exclusive content.
Or start shooting assignments. Again, if you have the kind of signature portfolio that makes customers want YOU as the photographer for whatever they need.

I don't see any other options here?

Other alternatives include:

1. Direct selling via your own shop (see threads on Etsy and Shopify)

2. Print on Demand (eg. Fine Art America, Society 6, RedBubble)

3. Designer Resource Agencies (Creative Market, DesignBundles, Hungry JPEG)

4. Book Covers (see Alex's blogs and threads)


Upside. After about 6 months, its quite feasible on some of these sites to start earning as much as the middle tier agencies - with a potential to earn more. Once you're in, there is no reviewer system. You set your own prices. Lower or no agency commissions. (Not sure about book covers)

Downside/s: Learning curve. Needs research to understand what buyers need. May have to change what you shoot. Some places are very choosy about who they accept. Without a reviewer system you have to become your own reviewer and may have to raise your quality standards to increase sales. Without an agency between you and the buyer you may have to put up with demanding buyers who can drive you crazy. You may have to do your own marketing. Site fees/costs on direct selling sites.

Bottom line. After all of this hard work and effort, you may start to appreciate what agencies actually do for us. Although I still can't see how some of them justify taking up to 85% of our income to do this.

And yes, we need more agencies that allow us to set our own prices. That's the main benefit of most of these alternative venues above.

Very useful Annie, thanks.

Maybe one addition, all of that requires - from my point of view - the shift from "taking" a shot to "making" a shot.

You show up at the right place at the right time, you have the patience and timing to push the shutter button at the right moment, you know how to frame your composition, you know how to operate stealth, you have the gear and ability to pull it technically off under conditions which you have little or no control over. 
All of that enables you to "take" fantastic shots, thinking landscapes, street, documentary or journalism for instance, which can do very well at "numbers game" microstock, but I think (correct me if I'm wrong) a lot of that is less suited for POD, book covers or the other designer oriented markets you mentioned.
Of course, well framed landscape shots or specific architecture can still do well for book covers or POD, but the options are more limited.

Your game requires an additional talent or skill. You have the creativity to come up with a conceptual idea and construct or direct a scene in a controlled environment like a studio.
You first "make" you shot, based on knowledge about what creative buyers need, and then "take" the shot. Great for Microstock, but maybe even better/less frustrating for creative markets because they offer RPD?

Both are different disciplines and one is not better than the other. Very often, both disciplines are covered by different people.
Think food photography for instance. The one I know has a cook, a set designer and a photographer. All very skilled in their own discipline.
Of course, they don't do microstock, they do assignments for major food brands.

In the end, speaking for myself here, it still comes down to upping your game by developing an additional skill.
And my observation is that people who keep on developing their skillset, or treat it like a business and hire additional skills, grow out of microstock and find different, better paying markets.

That said, kudos for you that you can all do it by yourself, and be successful at it!
In my book, that's a very respectable achievement.