Ah, a place I want to return to - Central Asia! What about Uzbekistan too? ;)
Interest regarding scenery and culture
Tajikistan is basically a country on mountains. Kyrgyzstan has the flat area around Bishkek, but quickly climbs in any direction out of there. Kyrgyzstan has the lakes (Issyk-Kul is stunning, like a Kyrgyz Cancun!), while the trekking in Tajikistan is superb! Of course, if you're heading here and can, you'll want to hit the Pamir Highway (M41) between Kyrgyzstan and Tajiksitan in the east of the countries - follow in the footsteps of Marco Polo!
Kyrgyz culture is very much like Mongolian, with the more nomadic culture. They have yurts - movable tent-huts. The food is heavily oriented around meat, especially lamb shashliks (kebabs). Tajik is more rice and crops, but also beef/lamb in stew or plov. Generally I found the Kyrgyz food more varied, interesting and tasty, however.
Tajikistan is cheaper than Kyrgyzstan. The Lonely Planet claims that the average wage in Tajikistan is $2 a day, but I and others would debate this. However, it is cheaper. The food is repetitive (you'll grow tired of plov very quickly), but there are supermarkets and markets available.
Ease of reaching the country from Europe (Germany, France, Netherlands or Belgium) by air.
Flights into Almaty in Kazakhstan are common, and then connecting flights to Bishkek or Dushanbe are the easiest. However, a useful and seemingly little-known fact is that Baltic Air has regular flights in and out of both Bishkek and Dushanbe, from/to Riga, Latvia. Most European travellers leaving/arriving were using this route, and then connecting from Riga to their home.
Kyrgyzstan has CBT - a group called Community-Based Tourism to try and make sure the incoming money makes it back into the communities. However, some viewed their prices as rather inflated.
Tajiksitan - not so much, there are companies around if you search enough though, including tours from Khorog up the Pamir Highway. Often locals will suggest that their sister's husband's cousin's son could be your tour guide, for a nominal fee...
The possibility to travel independently
Both are possible. Both are not easy if you don't speak the language - either local or Russian, but as I and many others I met there can prove, it's certainly possible to do it completely independently! And you'll have some fantastic stories afterwards about when it inevitable goes wrong (I tried to evac one city for medical reasons, and my urgent flight was cancelled due to a sandstorm in Dushanbe, leading to a 16 hour road trip in the back of a Landcruiser...)
The ease of entering the country (visa procedures)
Tajikistan requires an entry visa to be obtained in advance. Visas are for 30 days, and although it's arguably possible to extend this in Dushanbe, I've seen the act of people trying to get visas in Dushanbe cause breakdowns and tears. Backpackers! Bishkek in Kyrgyzstan, however, it's possible (citizen dependent) to obtain a visa as you arrive at the international airport. Also for 30 days.
Do you really want to know? ;) Tajikistan has a problem with drug running from Afghanistan, and as such the border is a crazy, crazy place, especially around the two routes between Dushanbe and Khorog, where landmine warning signs abound...
Kyrgyzstan doesn't have those same problems, but I found the police worse here, and in both countries you have to have ALL your papers on you at all times, and be prepared to be searched, harassed and accused of things. Don't give in tho - you're in the right, and you have no need to bribe.
Saying this, I did have a vehicle accident in Bishkek where our bus hit a car...but hey, all part of the fun ;)