Comparing a desktop round cell charger to a hobby charger is like night and day. Desktop chargers are typically limited well below 50W output where even the least expensive hobby chargers start at 50W. The hobby charger I use (Turnigy Reaktor) is rated for 250W output.
Hobby chargers have a number of features you don't find in desktop chargers designed strictly for round cells. For example they can do a wider range of chemistries including Li-Ion, NiMH, and lead-acid. They can do Li-Ion packs (multiple cells in series) with balance charging. They have diagnostics like battery IR checks and track charge input. Some of the standard features you find in hobby chargers are making their way into desktop chargers now, but they're still lacking.
A down side with a hobby charger is you need an add-on cradle for use with round cells. Also hobby chargers typically require an external 12-24V DC power supply, however hobby chargers with built-in power supplies are available. Hobby chargers require a lot of manual input such as cell chemistry, cell counts, and rates.
In terms of convenience a desktop charger is probably going to be best. In terms of features you can't beat a hobby charger.