Right now, Strategic Cruisers are much more effective at providing links. The easiest comparison to look at is the Loki & Claymore. With the Loki Defensive - Warfare Processor subsystem, the Loki gets 5% bonus to effectiveness of Skirmish Warfare links per level. The Claymore only gets 3% per level of Command Ships. Right off the bat, that seems like a problem to me. That's especially true given that the Defensive Subsystem skill is a 1x multiplier versus Command Ships 8x, and Command Ships require a much larger skill investment overall with Racial Cruiser and Battlecruiser V.
This isn't even the start of the problem though. Tech 3's are incredibly versatile. Anyone who is using a T3 as a pure booster (alt) will clearly set it up with the Covert Subsystem and likely an expanded probe launcher. This can easily be setup with 3-4 warfare links to boot, no problem. What you get out of that is an unbelievable advantage: a ship that can launch probes, cloak up, provide a warp-in and then GTFO and boost you to victory. That's a pretty awesome advantage for "solo" or "small gang" pvp.
The Claymore, on the other hand, has almost none of those advantages. It has the lower bonus for warfare links and none of the cloaky-warp upside. You can fit an expanded probe launcher on it, but it has no bonus for scan strength of probes or fitting requirements. It can field three warfare links without need for Command Processors, but the Loki has no problem tacking on two or three of those to get the links fitted. The only advantage currently to Command Ships is that you can fit these three links without gimping a combat fit. But with boosting as it stands today, very few people bring their link-fitted ships on grid anyway.
This whole deal doesn't seem quite right in my opinion. T3's should not outdo Command Ships in the role that CS's were designed for. Strategic Cruisers were meant to be a jack of all trades, not the ultimate ship for every task. The balance is clearly off.
What's the answer then? There are a few options. First of all, if RJ's proposition of ending off grid boosting goes through, the problem would solve itself in terms of balance between these classes. No one will leave a gimped Loki on grid to get primaried, but the Claymore (and other fleet command ships) can hold its own, especially with appropriate Logi to prop it up. But if those changes don't go through and off-grid boosting remains, the bonuses on these ships need to be changed to bring them in line. Either Command Ships need a buff or T3's need a nerf or maybe even both. A cruiser should not be beating a dedicated bonus-providing battlecruiser hull. No questions asked.
I hope CCP takes a look at this over the next few months (years?). Its not necessarily an overwhelmingly important fix, but the current situation is out of balance nonetheless. Give Command Ships back their rightful place in fleets and as off-grid alts!!