Don't be affraid to look at used opitions on ebay and craigslist. If you can be patient and look hard you can get great deals on much more expensive speakers still in really great condition. Speakers that are built well can last many many years. Also drivers haven't really changed much in the budget realm for years now so new designs may not sound much if any be better. All I'm saying is don't overlook those 10 year old bookshelves that cost $1500 when new but could be had within your budget today just because of their age. Just research online and know what you are buying (I,E. find out if their are any pitfalls to watch out for with the design like rotting foam driver surrounds instead of much longer lasting rubber ones.)
With that said I have a bedroom 2.1 setup with the Pioneer SP-EBS73 -LR and I love them for music and movies. I picked up the Pioneers on Ebay used but mint for $140 free shipping which is like $260 off retail. These would allow you to have a shot at atmos when you expand to 5.1. The Pioneers sound very detailed (like the Klipsch you liked) but not bright and put out an amazing amount of clean strong bass for a 5.25" woofer. Also the concentric mids and tweeters in the budget(Pioneer and Elac) and high end (TAD and KEF) speakers, all designed by Andrew Jones, have nothing but strong reviews. Again I love mine.
I can also recommend anything from NHT. My main theater is 5.4.4 built around 17 year old NHT's. My 2.9's will hit reference with very little strain if any and to boot they are some of the best music speakers that have sent their waves my way. Also the little sb-2's I use for overheads were smooth and impressive during a stint in my 2 channel setup. I picked up all 4 sb-2's (in paino black no less) for $130 off ebay. Used of course.
Of the new options you listed I would choose the Klipsch you liked. When I was 18 my first setup was a cheap Yamaha reviever and Klipsch synergy bookshelves. I liked them quite a bit but found I liked a smoother sound as I got a little older and moved away from Klipsch. I have read a lot of good things about the new lines (like the tweeter's are smoother sounding now) but have no ears on experience.
Not sure your time frame on a sub but it will take a lot of strain off what ever speaker you choose. If you can squeeze a $100 or $200 now the Dayton sub1200 ($128) and sub1500 ($198) have been measured to be a decent little sub for the money. But again my strongest cheap sub recommendation would be not a cheap sub at all. Look at what you can find local used and on ebay. Find someone upgrading and you could really score a strong (expensive when new) used sub cheap.
Just for some more" buy used encouragement" I estimate about 92% of all my electronics were bought used with a single failure. (knock on wood) But have had 2 new components die in less than 2 months. Prob bad luck but food for thought none the less.
Goodluck and may audio nirvana find you in the new year my AVS cohort!!!!