Disintegrate, Reconstruct, Necrotic Ray, Mass Suggestion and Greater Heroism are all very important spells. GH and Disintegrate are absolutely not negotiable. so the level 6 slot is actually very competitive indeed.
your level 5 slots (of which you have more!) would be a choice between Eladar's Surge, Mind Fog, Hold Monster, Protection from Elements, and maybe Symbol of Pain or Dismissal. and Ball Lightning, of course. of these, only Protection from Elements is a "must have", so you're fairly free to pick and choose what you want. in essence, your level 5 slots are "cheaper" than your level 6 slots -- both because you have more of them and because there are fewer important spells competing for them.
also, Heighten is actually cheaper to use than a higher level spell -- that's why the feat with its enhancements exists in the first place. Heighten is an unmitigated "good thing".
now as for the particular behavior of Chain Lightning in DDO, the description is actually quite vague. in PnP, the primary target takes full damage, while secondary and tertiary targets etc. take reduced damage (this spell is the originator of the unique concept of "chain" behavior where damage is progressively less for each subsequent target). so while the first target would take 20D6, the next only saves against 10D6 and the third 5D6 and so on, and the spell had a limit on the number of targets it could affect, while "ball" spells hit anything in the area. so... in DDO, the description does say that the primary target is subject to (1d3+3) for every caster level, it only says that subsequent targets are subject to a "similar bolt". which is ominous indeed.
personally, i have found that DDO's Chain Lightning is finicky in its targetting behavior, and unimpressive damage-wise. especially when compared to various Acid spells which have much better damage:SP ratios (not to mention the Dairy Queen being weak to Acid, as well as many other powerful creatures with elemental resistances...). when calculating the damage:SP ratio for Chain Lightning, you should remember that you are only gaining those last five dice once you're past level 15, and Chain Lightning costs the same at whatever level you are... and it costs more than Ball Lightning no matter what as well.
if you really want to be conservative with your spell slots, i would recommend that you take Lightning Bolt and Eladar's and leave it at that! Bolt's path is wide enough to be functionally similar to Ball but it's cheaper still and can double-hit, and Eladar's has superior single target damage than any other electric spell anyway.
nukes are like ___________s: all you need is one good one to get the job done.