We do it on percentage of ownership.

Many associations allocate by square footage. Many others, equally. Things to consider - what components would cost more to repair or replace because of the difference in size.  
 
 
 
Sometimes HOAs use equal for all administrative charges, but varied assessments for water use, construction costs, reserves and the like.  
 
 
 
Just a note, be sure to check your current documents. You may need lender approval in addition to owner approval if you change the pro rata share of assessment responsibility - and it is hard to get.

I would recommend that you take your current documents and have an attorney give you an opinion. It is a legal document and you will need an attorney to correctly take you through the process and file the documents. Don't try to "cheap out" by doing it yourselves, and don't go with an attorney that has no experience with Associations or with amendments. 
 
 
 
You also don't have a lot of info in there. What is the HOA responsible for? If it is only common areas open to all members, the size of units/homes should not even apply. Basically, they would be open to use to all so they should probably be equal. However, if the maintenance is for the units as well, then it is unequal and it would be recommended to have a percentage of value which is determined by varying factors, and the factors will need to be determined and then the percentages can be set. In my understanding in various states, usually they must equal 100%. 
 
 
 
Start with an attorney. That is your best bet. Also, be aware that if you determine that this is warranted, it is usually a lengty process of 1-2 years.

if you're talking about 'common charges' ... there might be simpler ways to better allocate common charges, than by changing the formula you already have. often the percentage allocations never considered what real expenses would come along and who truly benefits, and when they do, the percentages don't 'seem' as fair. check your docs and see if there is a provision to allocate certain expenses to only those units with that special asset, like a garage or balcony. often we get too picayune about expenses, and in the long run, and pragmatically speaking, it all balances out. if you feel shorted, just make sure your unit's common areas are being fairly taken care of in the budget ...

Why are condo fee's set by the Sq Ft as to how much your condo fee is. The condo fee's cover the common area and streets as well as other common area places. Don't you think everyone should pay the same amount????