For the last several years I have been a competitive age group multi sport athlete. Two years ago I was severely injured in a high sped car wreck while in a cab. I miraculously recovered but am unable to run so I switched to aquabike, which I have excelled at - been on the podium every race since my recovery and won most of them. But a combination of things - really rewarding but demanding job, kids doing competitive travel sports, etc. had me questioning whether I would continue racing. Then I was in a really bad bike crash that left me and my family ready to take a break from the road for a while. So, I have “retired” from racing and am working out exclusively on the trainer. My intentions in working out are 100% just to stay really, really fit. I have also used this as an opportunity to start being better about general fitness - weights, etc. And I will continue to swim once my wounds are healed enough that they let me back in the pool. Since I am no longer coached, I signed up for TR and jumped into a mid volume build, which I planned to follow with the general fitness specialty then maybe base. But my question (finally- sorry for the long post) is whether it makes sense for pure fitness to do a training plan with periodized training, etc. OR should I just work out, just mixing in 2-3 intensity based workouts with some endurance and cross training on other days, with a day of rest and a day of active recovery? And should I ever be doing long (longer than an hour or hour and 15 minute) trainer workouts, even on weekends? Have been doing the 1.5 hr workouts on the training plan last couple of weeks, and am fine continuing that - just don’t know if that is beneficial for general fitness or I should keep it a bit shorter? Thanks.
Sorry to hear about your accidents and bad luck, hope you recover quickly. I doubt you’ll ever lose your racing/competitive mindset, it’s seems engrained in people like us. I’d recommend Zwift racing in the future when you feel up to it.
Regardless if your working towards a race or not, periodization is an effective way to build fitness. You may not need to do Specialty, but there’ no harm in doing so. Since you’re not targeting anything, you have many options. I’d recommend Base - Build - then either Specialty or back to Base - Build. Allowing a few weeks of non-structure after Build or Specialty.
If all you are looking for is basic “health & fitness”, I’ve read that it’s best to simply train at/below VT1 (aka Zone 2/Endurance), and the 1.5hr workouts would serve you well. Performance gains are a different story.
I feel like your a better candidate for Zwift than TR, as you don’t really have a “goal” in mind per se. I would think keeping yourself from getting burned out would be the best strategy. Unless your pretty mentally focused, I would think doing base builds specialty etc. over and over without a real way to gauge or perform at a high level and try to accomplish your goals would be a quick way to make this into more of a chore. As it is, structured training can be pretty demanding and if you can just crank out structured training on the trainer for fun long term, I envy your mentality (or pity, not sure).
Your goal is to be “really, really fit” so I would say structured training is for you. 
It’s not clear how disabling your injuries are now, but I would consider what is needed to rehabilitate or maintain health first, and consider cycle training in addition to that (I’m thinking some kind of strength programme for example)
For general fitness I’d have thought an approach with a lot more variation than just cycling and swimming would make sense. I would really mix things up. Do some yoga and pilates. Lift some weights. Get a TRX. Do some CrossFit. Do some indoor rowing. Get on the climbing wall. Try martial arts. And for general fitness I don’t see any need to train one thing at a time for over an hour unless you want to. If you’re not doing multi-hour races then you don’t need to do multi-hour workouts. Once you step away from the endurance community you realise there are some very fit people out there who got that way without training for hours at a time.
(Obviously all the suggestions above are subject to whatever the docs or PT recommend you do and don’t do)
Thanks to all for the replies. So first - I do use zwift and have and will do zwift races. But I like structured workouts a lot - I can’t just ride on zwift all of the time. And I am mixing in other types of exercise - particularly on the endurance days. Doing indoor rowing, elliptical, etc. I am also doing weightlifting, TRX, etc. I hope to be able to run again at some point. Just not sure. My injuries were bad - broken neck, back, pelvis, femur, TBI, etc. but all healed really well except for my hip - my hip labrum is all torn up and that makes running really tough. But we will see. I will stick with the training plan, maybe with modifications to cut down some of the longer cycling workouts and add in some cross training those days etc.