It's hard for me to make a comparison between the original Marvel series and current Transformer comics mainly because I haven't read any current series however I'd recommend the Marvel series to anyone who has a slight interest in Transformers because THIS is what started it all - or more specifically Bob Budiansky.

My two favourite issues are #24 and #25, the deaths of Optimus Prime and Megatron. These issues had a bigger impact on me more so than TF:TM.