TL,DR - check out the last sentence of this post.
Survivability resources and the undervalue of everything else
Death Strike and our diseases are our survivability abilities and they compete for the same FU resources. Blood runes are also a source of survivability, although indirectly through Blade Barrier. This sets up a situation where FU runes are highly coveted and where we don't necessarily care how we spend our B runes as long as we can get them on CD for Blade Barrier.
The Pawning Off of Responsibility: the survivability vs survivability game
We can either put up the standard tank debuffs (STDs) via Icy Touch and Plague Strike or use those two runes for a Death Strike. I believe we are the only tank that has to make such a choice and its usually either a non-choice or a choice that we try and pawn off. In the first situation we can look at the math between the choices and choose the path that leads to better survivability - this is similar to how dps would choose between two dps abilities or talents and one would always loose out. In the second situation, we can try and get other classes to bring these abilities for us. I do this all the time, but I have the luxury of 3 hunter pets and a dps dk in my 25 mans. This principle really started to annoy me last night during Heroic Halfus though. I was tank swapping Halfus with another Blood DK and we had it so that the OT would be in charge of maintaining diseases on Halfus while the MT would just focus on Death Strike. This dramatically made it look like we are designed in such a way that not supplying our own STDs is by far the best survivability 'choice' we could make. If a DK wants to maximize his survivability he gets other people to supply his STDs. If say a Warrior wants to maximize his survivability, he can apply his STDs and not take a hit in survivability, he just takes a mild hit in threat. I'm all for not having classes being the same, but is the DK design a good design?
FU rune abilities are loaded with meaning, B rune abilities are whatever we can use to get them on CD.
This lopsidedness isn't my favourite design as I'd rather have all my abilities to have meaning. The most obvious way to shift meaning onto Blood runes would be to get them involved in disease management.
Old Death Knight Abilities - lessons from the past
My suggestion, at the bottom of this post, has been in the game previously, so lets take a look at its origins.
Pestilence - pre 3.1.0
When DKs first came out, Pestilence was designed to spread disease AND do damage. This was changed to its current form in patch 3.1.0 as it was ruled that DKs do too much AoE damage as it was (full strength diseases anyone?) and no one was really using Blood Boil because Pestilence would spread diseases and hit for a decent chunk of damage. The logical AoE application was then to use one Blood rune on Pestilence and then with the fast refresh rate of Blood runes in the old system, spam the rest of them with Blood Boil. This doesn't work as well with the new rune system where one Blood rune will be on CD already, and both are on a relatively longer CD than compared to the old rune system. I don't know the answer, but ask yourself this question, thinking back to WotLK and then thinking about Cata: After spreading diseases with Pestilence, how many times could you spam Blood Boil (using just Blood runes) before the diseases fell off? ...Is Pestilence really a good ability for Blood?
Disease Management 3.1.0 - the glory of Glyph of Disease
3.1.0 blew open the door for easy disease management for tanks with the inclusion of the much coveted Glyph of Disease, and all it did was allow Pestilence to refresh disease on one more target, your primary target. One GCD and diseases were managed easily, which made it a favourite glyph of tanks that had other things to manage other than the burden of diseases.