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The Skyray, alas, didn't make the transition from ForgeWorld to Codex particularly well. It has several things going against it.

1) To be used as artillery, it requires a spotter. Fair enough, but as far as I can tell, all other 40k arty doesn't.
2) The best spotters (Pathfinders) are quite fragile. The hard-to-shoot spotters are either expensive (StealthSuit spotters) or take up a valuable Heavy slot ( Sniper Teams). Exposing the Skyray to use its own markerlights is an option, thanks to the AV13 front and that seeker missiles can be launched even if it gets stunned, but in general, it needs other spotters to get best value out of it.
3 (the most important). It's not as awesome as a Hammerhead. If a Skyray build can't perform as well as a Hammerhead build, then people will stream towards the Hammerhead, and away from the Skyray.

So, to be viewed "as good an option as the Hammerhead", it needs a few changes. I've identified what I consider to be the chief issues with the Skyray, and possible solutions:

1) More ammo. The railhead may get one shot, but it's submunition covers far more infantry and can be shot (depending on circumstances) every turn. The ionhead variant is weaker verses vehicles, but it gets more shots, again, every turn. The Skyray's chief armament can be used up in a turn or two of shooting, and the thing about seeker missiles is, to affect even moderately armoured vehicles it needs to bang off several shots, and it takes a barrage of missiles to affect infantry. More missiles could be tacked on (say, an extra 3 or 6), or it could have some kind of a reload option (say, forgo a turn of shooting/moving to refresh the rack)

2) More shots.  As the Skyray needs to bang off several shots to achieve the same affect as a Hammerhead, it will quickly munch through markerlights at an inefficent rate, which makes it less attractive an option than boosting the BS of battlesuits or Hammerheads. Allowing more seeker missiles launched from a Skyray per markerlight (say, 2 or 3) would allow a Skyray to fire the shots it needs.

3) Improved Seekers verses vehicles. Railguns are a must to defeat vehicles, because of their awesome strength and ap. Something needs to be done here, as even with more shots and more ammo, a lot more missiles need to be launched to match the effect of a railgun, and if the ammo hopper is going to run dry quickly then people will go to Hammerheads. Perhaps something like giving Seeker Missiles launched from a Skyray the Lance rule (to reflect the fluff from IA 3), would make them more attractive, as the lance rule in combination with More Shots would mean that  1-2 markerlights and 2-4 missiles , you'd get both penning and glancing hits.