It depends what you looking for. Slovenia is small country of population of Prague. Ljubljana is nice, but very small provincial city. Slovenia has breathtaking countryside, from mountains to deep valleys and karst formation and small coast. Proximity of beautiful Dalmatian coast of Croatia, Italy and the Alps makes Slovenia desirable. It has better, warmer weather in comparison of Prague. However, lack of larger cities, make it harder to explore the rest of Europe. Prague is in central location, it is easily reachable from Berlin, Vienna, Munich, Frankfurt, Budapest, Krakow, Dresden and Nuremberg. Prague is European metropolis with very good night life, jazz clubs, pubs, theaters, music halls, disco-techno-rock-alternative musics, gay bars and brothels. It is very liberal city with feel of freedom only matched by Berlin and Amsterdam. People do not care what you do and tend to mind their own business. However, it also comes with anonymity and crime in larger city and often overrun by tourists on the weekends.
Economically is Slovenia little more advanced than Czech Republic, it has decent middle class, and incomes are generally higher in Slovenia than in Czech. However, Prague in overall is much wealthier than Slovenia, it has high per capita income, but the rest of the country lags behind the capital and Slovenia. For foreigners the differences are little. Overall, there is a bigger differences between people who have money and not in CZ, than in Slovenia. There is a wider gap among various provinces, where Prague and Western Bohemia is very well off, while industrial areas of the north is much in economic depression, which makes Slovenia much better economically. Slovenia also uses Euros, and its per capita is about 10% higher than Czech.
This comes also third difference, where Slovenian success makes them rather very arrogant. They believe that they are better than anyone else in Central and Eastern Europe and what once used to be friendly country (it was loved by Czechs) is now rather disliked by everyone. Ask Croatians what they think of them... Czechs are not warm people either, but once they step out of their shell, they will be helpful and nice. I do not think it is the case in Slovenia toward foreigners. You will have much easier time to befriend Czech and definitely easier to hook up there as well, as Czech society is socially and sexually much liberal than Slovenia.
If you look for quality time, shopping, entertainment, education, it will be hard to pick differences, they will be case by case bases. Czech Republic has better shopping opportunities as it is much larger country with very well developed shopping centers that are among the largest in Europe (like Letnany, Chodov, Olympia in Brno). Quality of services and dinning are better in Slovenia, but getting around is easier in Czech with much denser road and train network and higher density of gas stations if you will own car. Food is better in Slovenia, but drinks are cheaper in Czech, where bottle of beer cost less than can of coke. Education will depend on your topic. Czech have very good engineering and science education, but other topics like economics and medicine will lag behind Slovenia.