I\'m working with a huge table which has 250+ million rows. The schema is simple.
CREATE TABLE MyTable (
id BIGINT PRIMARY KEY AUTO_INCREMENT,
I'll second @MarkR's comments about reducing the indexes. One other thing you should look at is increasing your innodb_log_file_size. It increases the crash recovery time, but should help. Be aware you need to remove the old files before you restart the server.
General InnoDB tuning tips: http://www.mysqlperformanceblog.com/2007/11/01/innodb-performance-optimization-basics/
You should also be aware of LOAD DATA INFILE
for doing inserts. It's much faster.