After rereading the original post, I realize that there were some specific questions asked that I didn't address so I thought this morning I wouold add to what I posted last night. Let's see if I can do better:
Paddle shifters vs manual shifting. I feature that I seem to enjoy greatly. Manual shifting, you have no choice, you have to shift, up and down, or you aren't going anywhere. The semi-automatic with paddle shifters, GREAT. You have to shift up, and you can shift at 2,500 rpm in a lazy sort of way, or you can hang onto your hat and pore the coals to it and shift at 7 or 8 thousand rpm while banging thru the gears, your choice. I must say it's nice not having to shift down and let the computer do it, but you can down shift just like your manual tranny if you want to. And a big plus, when you come to a stop, you don't put your foot down and take the chance of getting your pants cuff caught on your foot peg. And we all know what happens next.
As to the comparison between the 990 and 1330, I really can't say as I am a new owner (2 months) of my Spyder, but from what I've learned in this short period, buying a new 2014/2015 model with the 1330 motor was the right choice. Smoother, quitter, cooler running, better gas mileage, less maintenance, it's all good.
Ok, older vs newer. As above, I singled out the 2014/2015 model years because as it seems to me, Can Am has taken what they have learned since coming out with the first Spyder, and steadily improved on the design. Listened to their customers and upgraded every year. Adding features and correcting problems. Maybe not as fast as some would like, but actually doing a pretty good job of it. Since I have a 2015 RT Limited, that is all I can actually talk about, or compare to. I like it much better than most motorcycles I've had, and since I try to ignore my 76 years, still tend to ride aggressively, so have to say, my 1966 Triump was more impressive, as was my 1975 Kawasaki 900 (not counting the 750 cc Kawasaki triple). My V-Max (the first one on the streets of Jacksonville) has to be one of the best all around motorcycles I've had, and the best has to be my Ducati ST4, although my last Harley (2010 Ultra Classic with some additions) was pretty close. This Spyder is very very good, and has all of the features that my Ultra Classic had plus, it has reverse that is power off the motor, not the starter, and I can back it out of the garage very easy, and not have to worry about holding it up while I make a turn while backing.
One last thing and then I'm done, wife wanting to ride. As I said, I've been riding since 1958, got my first bike in 1962, so it has been a while. I got married in 1975, (damn, that's almost 41 years, unbelievable that she has put up with me for so long) and gave her her first motorcycle ride. Anyway, I have tried, all this time, to get he r to learn how to drive a motorcycle, if only for the reason of being able to get us home if something happened to me. With no luck. She had no desire to learn how to drive a motorcycle, and went out of her way to prove that. But, she has now driven the Spyder 3 times, twice down our road (1/2 mile) and into the yard to the garage, and the last time she drove from the highway to the garage, which is close to 2 and 1/2 miles with some of it up to 45 mph. And, I have to say I am very proud of her for this, it was her idea. After the last ride she looked at me sweetly and said, "you know, if I decide I like this enough, you might have to see the bass boat so I can have my own Spyder".
I hope I've helped in answering your questions, and hope you have a Very Merry Christmas. But the Spyder, spend as much as you can afford, but you will spend more on accessories you learn about and can't live with out, Be patient, and learn to ride it as a trike, because that is where the beautiy is. Folks will drive by and smile, give you thumbs up, and tell you how cool it is. It's a wonderful situation.
David