If your sequencing budget is limited, and Transcript discovery is your priority, you could invest more in depth of sequencing and read length (>75Bp) rather than replicates. Also paired end data will be important. The assembly will only give you a snapshot of the input samples as well so if you think important transcripts are expressed in other tissues, conditions you may want to sequence those as well.
That being said, having replicates will allow you statistical power to quantify transcripts that are present in one sample/condition/tissue and not in another and look at differential transcript usage.
Here's a nice resource: