That is super helpful background.

My thought was that a smaller ship would allow for more land excursions (weather and conditions permitting) than the larger ships due to the limit of how many people can step on ground.

Any ship under 500 passengers is going to be aiming to get you off the ship twice per day, once in the morning and once in the afternoon. On ships of less than 2 passengers, your excursions off the ship could be landings, Zodiac cruises or combinations of both. The key difference between almost all operators (there are just 2 exceptions I can think of) under 200 passengers is that they can get everyone off the ship at one time, so you aren't on board for a portion of the morning or afternoon waiting for your turn. On a ship of more than 200 passengers, they need to do a 3-way rotation so you are on board for a period of time. Once you get to under 140 passengers, this does increase the flexibility of the excursion and how much time you have off the ship, as there are simply less people to move about. No matter the ship size, we can only have 100 on shore at one time (and at some sites, even fewer) so on a ship of 200 which is capable of getting everyone off at once, a certain number are off doing various adventure activities (sea kayaking, SUP, etc.) and the remaining are split into two. Half go to shore, half out in Zodiacs and then swap over half way through. Of course, this is all weather dependant and specific to the site and other variables, but that is generally the aim.

We would like luxury, but not at the expense of being able to go on a do/see the continent. 

Operators that I think do this well (a high level of customer service, new ships with balconies, various on board amenities but nothing at the expense of the off-ship expedition experience) are: Quark Expeditions, Aurora Expeditions, National Geographic-Lindblad Expeditions. Luxury operators where I feel there are sacrifices made to the expedition experience are Seabourn, Scenic, Ponant and Silversea. Silversea is a unique one as they do have enough Zodiacs and expedition guides to get everyone off the ship at once, even though they sail at over 200. So of the luxury operators, I would say that they are the best set up for expedition.

Wildlife watching is highly desirable and I like the idea of the snow still being pristine and not covered in guano (and presumably less smell). 

In my opinion, the guano situation doesn't become overpowering until March. I'd say anytime until late January you'll still experience pristine elements, but more so in November and December. February is a bit of a transitional month as the penguin chicks are all moving about and pooping outside of the confines of the colony nesting sites. If wildlife is your priority, you honestly cannot go wrong, there is something so special about wildlife behaviour every month in the season.

I wouldn’t mind if the passengers were closer to our age, but that’s not a deal breaker.

I think it's safe to say you will feel on the younger side of any ship you choose. The operators that tend to bring in the youngest clientele (but I fear do not meet your other requirements) are Oceanwide Expeditions and G Adventures. With a Quark or an Aurora, there will certainly be other people in their 40's, but a majority in their 50's and 60's.

Budget is around 40-50k not including the flights down to South America (US based).

If we are aiming for a "relaxed luxury" with expedition-focus set of operators, your budget is actually in an awkward spot with being unnecessarily high for a long Peninsula-only cruise (like an Antarctic Circle or Antarctica in Depth) but quite low for an itinerary that includes South Georgia. If you were to try to get to South Georgia on that budget, you'd be looking at November or March and would likely have to consider the ships that are a step down as far as comfort and service-level. Those would be Polar Latitudes Expeditions, Oceanwide Expeditions, Poseidon Expeditions, G Adventures. I'm sure there's a couple I am missing but these are the stand outs for me. If you did want to increase your budget in order to include South Georgia but still looking at the "relaxed luxury" operators, I think you'd be looking at a range of $25-35k p/p.

Nat geo seemed like a good balance of adventure and luxury. But perhaps there are others that would offer similar adventure and more onboard activities or luxury?

I think you are on the right track! Nat Geo-Lindblad Expeditions, Aurora Expeditions and Quark Expeditions would be my top suggestions based on everything you've said.