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Zicatela is actually the quietest beach I visited in Oaxaca, there are miles of it with no development and not a soul in sight. The Escondido end is touristy but the southern end is where the backpackers are these days and the vibe was mellow rather than crazy party. The middle is miles of deserted beach.

A car is pretty handy if you're comfortable with the driving and cost. I've done the bus route and rented cars for the area you are looking at; just having an AC equipped car when you exit the ruin is worth a lot.
There are two ruins east of Xpujil or west of Bacalar depending on where you stay, Kohunlich and Dzibanche are nice ruins. Dzibanche is a big complex with outlining buildings as much as a mile or two away, all on the blacktop so a car in convenient. One can see Bacalar from the big pyramid at Dzibanche and a faint outline of an old Maya road heading that direction.
There are a number of small ruins west of Xpujil, Bacan being the biggest one-it has a moat, not a common feature in Maya ruins. The monster masks in that area are the best.
Calakmul is a big ruin, take a day pack with extra water and pace yourself, there is a lot of walking involved and as much climbing as any normally fit person could want
Renting a car, you can spend a week visiting ruins in the general Calakmul area. Buy a styrofoam cooler for the trunk of the car, cold drinks are a real pleasure in Yucatan.

I've been thinking about this so much.
#1 In the past, connecting on the bus with folks was one of the best ways I had to actually get a sense of the people in the places I visited. (I'd be taking the first class ADO when possible.)
#2 I haven't done any planning, so having some downtime on the bus to trip plan on the road would be super helpful
#3 I'm not young anymore (43) and haven't had a real backpacking trip in over a decade. Comfy beds and AC are more important than they used to be.
#4 Time is limited.
#5 Car is $440USD+gas. I'm guessing I'll spend at least $300 between busses and taxis. So the $$ are not hugely different.
#6 I will want to visit cenotes and other points of reference. Last time I was in Merida, this was totally doable by transit. Assume the same is true most places.

Any advice? I'm unconcerned about driving in Mexico (I think the roads are great) and the money while important is only about $200USD over 10 days.

How difficult is the transfer from Bacalar to Xpujil (and Xpujil to Champoton)? Seems like either hire a taxi or go to the combi/collectivo station in Chetumal. According to this site there is a connecting bus through Chetumal that looks fine.

Zicatela is the surfing beach and the party beach. Avoid it and you'll be fine.

Unfortunately Mexican beaches are nothing like those of, for example, SEA. Their biggest downfall IMO is that they are generally devoid of trees and any natural shade. Obviously anywhere with parasols or umbrellas for rent is pretty touristy and may be not what you want.

I was walking along the beach in Mazunte before sunrise a couple of weeks ago and a swimmer was already in the water. Palm trees are set back at the edge of the sand, not next to the water, but you can rent a lounger and umbrella by the shore which is what the Mexicans do so they can keep an eye on their children.

Puerto Angelito and Carrizalilo are both calm beaches in Puerto Escondido. Playa Panteon in Puerto Angel. Playa Santa Cruz in Huatulco, etc.

San Jose del Pacifico makes a great place to stop halfway between the coast and Oaxaca on 175. Refreshingly cool.

The Viveros in Coyoacsn has no traffic (except for other pedestrians) and is quiet and peaceful.

when you go to Coyoacan on day my recommendation is to start they day in san angel and walk to Coyoacan: avenida la paz, arenal, francisco sosa. the last avenida, especially, goes by very nice old houses and takes you all the way to coyoacan. we found it to be a very lovely walk, with very little traffic, I would highly recommend it.