I agree, sometimes fine line and might be a little subjective, but that is how I look at it.
This line was also relevant in my post.
In the end, this is all subjective. To me, several of your proposed tweaks change the core rules, while I propose stuff (as Solomoriah has said regarding the new upcoming 3rd edition) that does not invalidate or change the core rules... but simply layers onto those rules. Perhaps that is the better way to describe my paradigm.
I would suggest things that layer upon the existing class framework without changing the nature of the core rules as written (when possible).
For instance,
Adding Cantrips does not invalidate anything in the core rules, only adding to the MU
Adding bonus spells for prime requisite does not invalidate anything in the core rules, only adding to the MU (or cleric appropriately with Wis).
Adding Arcane Bolt does not invalidate anything in the core rules, only adding to the MU
However, adding or changing actual weapon proficiencies
does change the core rules as written.
Changing the nature of armor or simply adding armor for MU
does change the core rules as written.
To me, arcane bolt is a new ability (add-on). It works like a weapon (about like a thrown dagger) more so than a spell, basically an unlimited thrown dagger... already doable by the MU, just not with the magical veneer. Perhaps we have differing views on how such ability might work. Here is the relevant paragraphs from my own house rules:
Arcane Bolt – All Mage classes may produce an Arcane Bolt once each round. This bolt may be used either melee or as ranged attack (10/20/30) and deals 1d3 points of physical damage. The Mage must roll to hit, with his or her Prime Requisite modifying the attack and damage rolls. The damage type dealt is a generic concussive force like a sling bullet.
At each level divisible by 5 (IE 5th, 10th, 15th, etc) the Mage may add another type of damage that can be chosen from round to round. Such choices include Fire/Heat, Cold, Electrical, Sonic. In addition, one could choose Necrotic or Negative energy causing damage to living tissue like a Cause Wounds spell, or Living / Positive energy which damages undead. For either of these positive or negative energies, the bolt does not produce healing effects (whether to living or undead respectively)
Adding a new proficiency like Crossbow to the MU, substantially changes the MU with regards to range. Bear in mind I am not so against this as a potential change to MU, but I was putting forth examples of each... not trying to dictate the choices of changes/tweak for your document. I would actually be quite fine with MU's with light crossbows or slings (but thinking sling is better suited).
In that sense, adding Short Sword to MU would not bother me either (Gandalf had a elven sword - I would even say longsword by the look/description - Glamdring)