Both give different feel, both leaves different impression, but the structure of both are based on the French novel The Count of Monte Cristo. Both are mysteries.
In both a person will be isolated from the rest of the world with lots of gold for many years (not even a minute of sunlight). Followed by revenge, then MC changing that person.
Kindaichi focuses on trick, guessing, thinking. Gankutsuou more on human relations.
**In Kindaichi only the first four episodes are common with Gankutsuou.
Both are long running series that dealt in mysteries of crime, where it involves youngsters investigating it, however Detective Conan is still continuously running series, while Kindaichi is often divided by seasons.