You can use the GParted live CD to boot up the old VM and delete the system partition and resize the data partition to take the free space release by the system partition deletion... and another option is to use vCenter Converter and select convert just the data partition. Take a look at GParted: GParted -- A free application for graphically managing disk device partitions
Note that using vCenter converter you will need some additional free space on datastore to store the new vmdk and that the process of V2V choosing only the data partition will finish with failure status, since the system partition was not copied, but you can ignore this message and get the new vmdk.