It is impossible to put every upgrade on your armor and depending on what you are doing you might have different armor for exploring and killing monsters. Having your armor full of useless traits is no good and trying to force certain traits on to the armor would take forever and would be a nightmare. Fighting monsters may give you Fierce Strike, but picking up experience might also give you Experienced which might not be so desirable. Luckily there's a way to pick and choose what traits to level up and what enchants to remove.
Crafting the Draft of Angelus will boost the number of upgrade points your armor can have by a maximum of 200. Now, this is only a quick fix and can help to collect more Upgrades and level up other upgrades.