I first realized that the maneuver penalty from armor affects weapon skills (as they use the Agility stat). The problem with this is that a character's DB is also highly determent on their OB, which in turn is determined by their weapon skill: so by taking a penalty to their weapon skill, are they not effectively lowering their DB, the exact opposite of the goal of armor?
Almost enough said on this. Of course, the maneuver penalty lowers your DB, but the DB bonus gained by the armor is high enough to counter this. There are more developed rules concerning armor in "Martial Law". In addition to the bonus, heavier armor reduces the amount of damage (all aspects) while light or even no armor increases it.
Also, for characters with low QU bonus, armor is the best chance to get a high DB (they are hardly effected by the penalties, if at all).
Of course, heavy armor reduces one's ability to move (and believe me, as an active swordfighter I can ensure you on this!), so its perfectly OK to have one's OB (and therefore the capability to parry, i.e. increase DB) reduced.
This also lead me to try my hand at making my own armor (something I was looking forward to with HARP ever since I heard of it). But the end result, shall we say, was a grievous disappointment. Mixing and matching among the Chain, Rigid Leather and Soft Leather pieces, I came out with a suit of armor that was just like a full-set of Rigid Leather, only worse (higher MinMP, higher CP). This greatly perturbed me.
It also eventually dawned on me that clerics would take Cost Penalties for magic just like any other spellcaster, something I was not counting on. This also leads me to what a mess, as it seems to me, that is the magic scaling. Flipping through the spells, I began to cringe a little at their overly-generic names, but even more so at the questionable merits of scaling, particularly when you are trying to scale damage. The healing spells, as I believe others have pointed out, are incredibly odd in their effects (I was instantly given the image of a tank-dwarf charging into battle with two clerics following close behind like something from Team Fortress). Though it is a very rare moment, I hate when I have to exclaim while reading an RP book "What were they thinking?!"
Concerning MPs, I absolutely disagree on your comment. I've found it highly entertaining and rewarding to customize armor and I usually end up with much better and more sensible (character back ground oriented) results than by taking a full set (I do have problems with certain pieces of armor though, e.g. chain boots).
The CP will almost always be higher whit custom built armor. "College of Magics" explains, that the magic energy is more easily focused through a single homogenous obstacle (full set) than through many small heterogenous obstacles (custom made). As a rule I agree on that, but I also like spell casters not to wearing heavy armor, but using spells to better their defense.
Your cleric will have to deal with the same problem of CP, not when his god sends him the power, but when he casts the spell himself (also explained in CoM), but you may well design a talent reducing the CP for clerics (something similar has been introduced with the paladin profession already).
Personally, I love the HARP magic system. Playing for 18 years now and having played well over a dozen different systems, I consider this the absolute best. With the possibility of scaling each spell to your wishes you have an incredible flexibility when it comes to spellcasting. At the same time you can scratch those stupid spell lists in RM, where the same spell could be read up to tenn times with only a little more effect attributed to it. If you don't like the "overly-generic" names, rename them (I actually was forced to this for my anglophobe and not anglophone players as I'm from and playing in Germany) and give them cool names. The system of learning a single spell and being able to develop it until you become a true master is great.
What you mean by odd effects of healing spells, I can't figure out. Same with the damge scaling, please elaborate.