The best way to get better at aikido is to train aikido. Period.
As far as your question, for upper body vs lower body development, I would answer: neither. Or more accurately "both". It seems that a good deal of aikido is moving the body as a unit, so it seems prudent to engage in supplemental training that works the body as a unit.
Personally, I'm rather biased towards squats, deadlifts, snatches, cleans and the multitude of variations of each of the movements I mentioned (for example: zercher squats, box squats, front squats, one-legged squats, hack squats, etc....) On the downside, these movements often require resistance, which means a gym or odd objects (kettlebells, sandbags, medicine balls, etc....) Also, if you've not familiar with these movements, a competant trainer to walk you through the workout is a good a idea for a few sessions.
If you don't have those things available to you, try Scapper's bodyweight workouts
Start with workout #1, and be prepared to WORK. For endurance, try Taku's interval training, listed on the same page.
As for solo training, I'm a bit of a heretic and say, forget it. If you can't train aikido with someone, improve your physical conditioning doing something you enjoy (dance, yoga, pilates, weight training, swimming, biking, hiking, etc....)
Anyway, those are my thoughts, take them as you will.