Putting off PhD for a (potentially) better experience I'm a software engineer for a CS lab for a top-20 school. I have a masters in CS (no thesis) from a top-tier university, a few secondary authorships and fairly decent experience working on research projects. I'm in a position where I either enroll in a PhD program at the school I currently work at or waiting a few years until my next chance to try to find a lab that is a better fit.

My wife is a medical student and in 3 years, she will be assigned a residency somewhere. While we are able to narrow down our choices to a handful of cities, there is no guarantee which one we will end up at. The PI for the lab I work in is aware of this, but has offered to let me do a PhD with him anyways. 

Pros:


He is fairly confident I will be able to finish in a few years and is comfortable with me doing my last year remotely (allowing me to move with my wife when she begins her residency). 
I like my PI and he treats the lab well
I would have a significant background in the research field having worked in the lab for a couple years by the time I start my PhD.


Cons


I feel my academic interests have little overlap with many others in the lab. I like looking for, analyzing, and writing code for novel algorithms as well as really thinking about how to go about creating software, I love to code and to explore the languages I use. Most of the lab's interest is more geared towards using, combining and writing scripts for data analysis tools, interpretation, pipelining etc. I could certainly stand to learn a lot from them, but I am just not as interested in that as I am in theory and software.
The lab is very young (not sure if pro or con). In the start of Fall 2020, the oldest lab members will be the 2 students in their third year.
I fear that a rushed and partially-remote PhD will be a lower quality PhD. 


I look at other labs, primarily those that are in the top of their field, and can't help but to be jealous of them. Just by looking at the publications, code and CVs of the grad students, my interests and abilities seem to fit in much better. I want to be in a lab where I can bounce software and algorithmic ideas off of the majority of the lab and get feedback and help on both research and software questions.

The question boils down to whether or not I should stay at my current university and do a relatively fast PhD with more perks/freedom or wait a few years and do a PhD in a lab that better fits my interests (and is potentially higher-tier as well). Obviously, there are risks associated with waiting. I may not get rehired at my current job and be forced to work in the industry for a couple years (I'm on a yearly grant, and I know money will be tight next year) or I may not be accepted to a school where my wife is matched for residency. 

I have debated reaching out to labs I'm interested in and asking them this question directly, however I worry it may seem like I'm going behind my PIs back or using him as a backup option. Would this be an inappropriate thing to do?

While I know this is a very opinionated question, I would like input on potential pros/cons that I am missing, other options, or perhaps even weighing in on what you think the right decision would be. If this post doesn't belong here, please forward me to a forum/site that is more appropriate.
It seems like you've laid out the pros and cons pretty well; only you can weigh them. But here is my analysis: 


  I feel my academic interests have little overlap with many others in the lab.


In my mind, this is the only valid con. It is difficult to do good work if you are not really interested in the project and don't share your advisor's goals. 


  The lab is very young (not sure if pro or con). In the start of Fall 2020, the oldest lab members will be the 2 students in their third year.


I see no real problem with this, given your positive comments about the PI.


  I fear that a rushed and partially-remote PhD will be a lower quality PhD.


By the last year(s) of your PhD, working remotely should not be a problem. 3-4 years in CS does not seem rushed if you already have a master's.


  I would like input on potential pros/cons that I am missing, other options, or perhaps even weighing in on what you think the right decision would be.


I think a missing pro is that you start right away. First, you don't know what the future holds; as they say, "A done PhD is better than a perfect PhD." And second, even if you had a guaranteed perfect PhD starting in three years, this means that you are delaying your professional life by three years. That's a long time -- only you can decide if it's worth it.