I tend to not think of this as contradictory, more along the lines of a new type of engine being introduced and disseminated throughout the Go'auld empire. Hence after season one, the use of ships becoming more and more prominent as opposed to gate travel.
For example, in season one we see Apophis traveling the gate frequently. He only had two ships to attack Earth and when he lost them it basically knackered him as a system lord and player until he stole Sokars fleet after killing him. but after season one, System Lords started having huge fleets and people were flitting all over the galaxy in no time at all, and the use of the Gate as a means of the Go'aulds moving about decreases.
I considered that, but it doesn't seem reasonable given the way the System Lords operate. If they had only just developed that kind of technology, there would have been a massive expansion of System Lord territories, as they reached out to grab many systems and planets they could never reach before. I don't think onscreen evidence supports this.
There is a lot of evidence that tells us ship travel has been common for a long time. Look at Aris Boch, who's apparently able to travel between systems with ease and work for whatever System Lord he feels like. And there are many references to people's fleets duking it out over the years. They couldn't have done so very easily if ship travel was that hard.
The only thing that really contradicts this is the fact that Apophis was devastated by losing two ships. I suppose this can be explained by suggesting that this was the last straw after a series of defeats by Heru-Ur, or that he put all of his eggs in one basket by having the majority of his Jaffa crammed on those two ships.
I think the real explanation is that the showrunners were originally thinking the same way as you-- that ship travel is supposed to be difficult and gate travel is easy, therefore gate travel is more prominent. They forgot this in later seasons as they introduced more ship-based stuff, hence the inconsistencies.