Yes, it pretty much would unless you already know the game. You're missing out on a lot of HP and Boff capabilities. The Heavy Cruiser (for example) has less hull than the Reconnaissance Science Vessel (the weakest Rear Admiral ship, hull-wise), and won't allow you to take advantage of your Commander-grade officer powers.
Also, you do NOT get discounts for fleet retrofits if you purchase a lower-tier version (the Commander Thunderchild does not give you a discount on the Fleet Akira, for example).
There is a small advantage in grabbing the lower-tier/rank C-Store ships, in that whatever console that comes with it can be taking off and put on the higher rank ships. The Thunderchild's Point Defense console is very handy, particularly when leveling a character, being able to put a lot hurt in several directions. The ship itself can be used for maybe one rank higher if you keep it well geared, but not beyond that.