1) Higher lvl of neatness skill only gives you option to destroy items 4/5th lvls, so no bonus runes from lower lvl items with upgrading this skill, but i think you get more magic crystals form low lvl items with upgraded skill. Even with only 1 lvl of this skill (needed for voice of dragon) you`ll get bunch of crystals from all 1-3 lvl items in game : 1 crystal cost 10k gold, and from most 1 lvl items you get at least 2 for 4000-8000 gold, it`s a bargain
2) Buying items to destroy with neatness is always better option then buying runes, expl : you get some 5th lvl item for 100k gold and you can get up to 3 runes/6 crystals from it. To simply buy 3 runes you need minimum 450k gold, and for 6 crystals 135k gold. Will you get refunded runes invested in skill by end of game maybe, maybe not but sure thing is that you`ll have plenty of crystals for all spells in game so it`s possible to save runes from alchemy skill, with 400 crystals you get from items. All in ll it`s good thing to do upgrading neatness after you get all mind rune skills that are important, and after you upgrade order/desortion/chaos magic skills to get option to upgrade spells and use all those crystals.
3) that`s nice unit setup and great for learning what every unit can do. Summon wall is great to start with, but sooner or later you`ll get to armies that are simply to big to stop with summoned units, especially with mage who have low leadership to start with (starting with Verona there are stacks that simply kill your summons in 1 hit and continue to destroy your main army before you get reload to summon again). Dragons arent `a must` units but are interesting to play with, but other then them try getting some meat shields to divert enemy units from your main army : royal griffins are great for this , guard droids also good when you have mechanics to repair them (just be careful not to waste his repair charges on summoned droids) , demon/executioners are also great to pull enemy agro as you have seen from demonologis summons. Try to drop thorns and take just 1 archmage, and go magic shield + stone skin on some summon in enemy lines (it`s ridiculous how low dmg they make) and dont use battle mage - it`s crap and gives no exp to unit, just magic shield and normal attack with occasional telekinesis to move enemy to trap/or away form some unit.
Good luck, have fun