You may think that 'nihongo-wo yoku wakaru' is more natural, because nihongo is not the subject. In the same way it seems more natural to say 'nihongo-wo sukidesu' instead of 'nihongo-ga sukidesu'. But we never say 'nihongo-wo wakaru','nihongo-wo sukidesu'. I noticed this strangeness when I studied Korean. Korean has particles like Japanese, and most of them correspond one by one with Japanese, but in this case the usage is different between Japanese and Korean. Korean uses a particle equivalent to 'wo' in Japanese in these cases. So, I think your doubt is very natural, and most of Japanese haven't even think about the strangeness. I don't know exactly why we use ga/wa when we say 'nihongo-ga/wa wakarimaru' and not say 'nihongo-wo wakarimaru', but anyway we say like that. I'm not sure your question is the choice between ga/wa and wo, or between ga and wa. In this case, you can use both ga and wa. Ant the difference of meaning is like below. 'Anata-wa nihongo-ga yoku wakarimasu ne' You understand Japanese very well. 'Anata-wa nihongo-wa yoku wakarimasu ne' You understand Japanese language well but...' this implies negative things such as you don't understand other languages, you don't understand Japanese culture, you can't play the piano....'

wa is usually put after the subject. So in this case, anata is the subject. ga is usually put after the object. So nihongo is the object. I've never teach Japanese grammar to someone, so my explanation is so bad.... but I hope it will help you.

Let me have a guess at this question :) I am just a beginner and don't know any better. あなたは日本語がよくわかりますね。 The particle が is used here because the verb involved is not an action verb. わかります (understand) does not involve any action. わたしはかばんをかいました。 I bought a bag. The particle を is used in this example instead because かいました (bought) actually involves action of buying the bag. わたしはうちで家族が四人います。There are 4 persons present in my family at home. Another exmple. います (present) is another non action verb. Thus the particle が is used.

I am also Japanese learner.In general Subject is marked by wa topic is marked by ga.In the above sentence Watashi is subject.Topic is something about Japanese so Nihongo "ga" is marked.This is what I know.

Hi, Mr.papasmurf. That is a good point. That explains many. A wa B ga wakaru. or A wa B ga sukida. These sentences are similar to reflective in romance languages such as 'Me gusta B' in Spanish. I would think about this structure in Japanese so that I can be fully convinced. Anyway, I want to analyse the usage of wa and ga a little bit more. Mr.A wa Nihongo ga wakarimasu. To Mr.A Nihongo is understandable. Nihongo wa Mr.A ga wakarimasu. In case of Nihongo, Mr.A understands. Mr.A wa Nihongo wa wakarimasu. In case of Mr.A, he understands Nihongo but ...(not other things). Nihongo wa Mr.A wa wakarimasu. In case of Nihongo, Mr.A understands but...(others don't). Mr.A ga Nihongo ga wakarimasu. It's Mr.A who understands Nihongo. (The answer for the question 'Darega nihongo ga wakarimasuka?(Who understands Japanese?)' Nihongo ga Mr.A ga wakarimasu. We can't say like this. Nihongo ga Mr.A wa wakarimasu. We can't say like this. Mr.A ga Nihongo wa wakarimasu. Usually we can't say like this. Only in a limited situation it may be possible. ex) Who understand both Japanese and Korean? Mr.A understands at least Japanese.