Spelling/Pronunciation anomalies tend to have historical roots. The "ea" problem is connected to what is known as the "great vowel shift" which took place around the 16th century. In Middle English, many words spelt
ee or
ea (spelling was not then consistent and both variations were found) were pronounced /eI/ - so "breed/bread" or "see/sea" rhymed with modern
braid and
say. During the great vowel shift these words changed their pronunciation - but the spelling remained the same. Others with the same spelling - eg
great - didn't change and retained the same /eI/ pronunciation as always.
Check
here or
here for more details.