Any honest solar collector comparison starts with the issue generally foremost in peoples' minds: cost.
In this regard, the flat plate collector will often come out ahead in terms of initial installation due to the simpler design and manufacturing requirements. No matter how inexpensive, though, if your system can't make sufficiently hot water it was not a good investment. While flat plate systems can be more than sufficient in warmer climates, their collection efficiencies fall significantly in colder weather as well as on cloudy days.
The evacuated tube solar collector in comparison will also see declines, but not nearly as precipitously as flat plate systems. As well as cost, a homeowner's solar collector comparison should include such factors as hours of available daylight, yearly temperature extremes and the collector space available should play a major part in your determination. Generally, if the local climate is mostly sunny and mild then the flat plate collector would be a good choice, but if in a colder and cloudier one then an evacuated tube system would be a better choice despite the higher initial cost.
Image: Willemferguson, via Wikimedia Commons
Further criteria for choosing the right collector
Another important solar collector comparison point is that of longevity and maintenance. Both types of collector can be mostly trouble free if placed and installed correctly, but sometimes issues do arise. The vacuum tube system can occasionally see loss of vacuum in a tube that must then be repaired or replaced, and could also face damage from thermal shock if the circulation is started after the heat tubes have run dry on a sunny day. These issues are simple to repair, however, since the natural modularity of the evacuated tube system means one need only replace the failing tube. The flat plate solar collector in comparison could suffer from freezing damage in especially cold weather, and any damage to the collector plate requires taking the entire collector off-line for repair or replacement.
While this quick solar collector comparison can be a starting point, educating yourself on the most common solar collectors for your area and their relative performance - the Solar Keymark is a good starting point - will better let you judge the options for yourself.