Note that doing a simple MINUS query between two instances will flag a lot more differences than you are actually concerned with.

Memory Configuration Differences

-- Memory Parameter Differences
select name, 
(select display_value from v$parameter@DATABASE1 where name=local.name) as display_value_1,
(select display_value from v$parameter@DATABASE2 where name=local.name) as display_value_2,
description 
from v$parameter
where name IN (
'sga_max_size',
'java_pool_size', 
'buffer_pool_keep', 
'buffer_pool_recycle', 
'large_pool_size', 
'shared_pool_size', 
'streams_pools_size', 
'db_cache_size', 
'') 
order by name

Optimizer Parameter Differences

-- Optimizer Parameter Differences
select name, 
(select display_value from v$parameter where name=local.name) as display_value_1,
(select display_value from v$parameter@DATABASE2 where name=local.name) as display_value_2,
description 
from v$parameter local
where name IN (
'optmizer_mode',
'db_file_multiblock_read_count',
'optimizer_dynamic_sampling',
'optimizer_features_enable',
'optimizer_secure_view_merging',
'query_rewrite_enabled',
'query_rewrite_integrity',
'star_transformation_enabled',
'optimizer_index_cost_adj',
'optimizer_index_caching', 
'optimizer_max_permutations', 
'db_file_multiblock_read_count', 
'parallel_automatic_tuning', 
'pga_aggregate_target',
'hash_area_size', 
'sort_area_size',
'bitmap_merge_area_size',
'sort_area_retained_size') 
order by name