First and foremost, the costs. Google Analytics 4 is free (except for the 360 version), quite the opposite, the cloud version of Matomo is paid. In both cases, there are implementation and management costs. Significant server-side configuration, maintenance, and updating work is required for the on-Premise version of Matomo (free for the platform),
Google Analytics 4 doesn’t allow the import of data from Universal Analytics version, that is outdated and non-GDPR compliant. On the contrary, Matomo allow only a partial import, the aim is to preserve historical data.
Matomo allows you to be the full owner of the collected data, with all the duties and privileges that come with it. On the contrary, when using GA4 the owner of the collected data is Google.
Google Analytics allows a quick and efficient integration with other Google services (e.g. Google Ads, Search Console, and BigQuery), while Matomo appears to have various difficulties in correctly tracking data from external advertising platforms (such as Google Ads or social media).
You can use both platforms for both web and app, but as far as apps, Matomo track fewer data than Google Analytics.
Matomo for Apps: there's still work to do
Much of the aggregated data for apps (such as sessions, users, screen views) are already available in Matomo. However, we recommend configuring the tracking scripts and events and setting up data anonymization options (automatic IP anonymization, raw data removal options, inclusion of opt-out features directly in the app).
Despite the aggregated data, up to now Matomo doesn’t track any data from apps, including acquisition reports from other channels (referrals, search engines, social networks, campaigns), automatic outbound link tracking, downloaded data, keywords used in in-app search, and other features like heatmaps, session recordings, A/B tests, analysis, and multimedia data attribution.